-/*\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.datamodel.*;\r
-\r
-import jalview.jbgui.*;\r
-\r
-import jalview.schemes.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import java.awt.print.*;\r
-\r
-import java.io.*;\r
-\r
-import javax.swing.*;\r
-\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
- public 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.\r
- 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
- annotationPanel.adjustPanelHeight();\r
- annotationSpaceFillerHolder.setPreferredSize(annotationPanel.\r
- getPreferredSize());\r
- annotationScroller.setPreferredSize(annotationPanel.\r
- getPreferredSize());\r
- setAnnotationVisible(av.getShowAnnotation());\r
-\r
- hscroll.addAdjustmentListener(this);\r
- vscroll.addAdjustmentListener(this);\r
-\r
- af.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
- case KeyEvent.VK_BACK_SPACE:\r
- case KeyEvent.VK_DELETE:\r
- alignFrame.cut_actionPerformed(null);\r
- break;\r
-\r
- case KeyEvent.VK_P:\r
- seqPanel.seqCanvas.increaseAARatio();\r
- break;\r
- case KeyEvent.VK_L:\r
- seqPanel.seqCanvas.decreaseAARation();\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
- seqPanel.seqCanvas.img = 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
-\r
- if (av.getWrapAlignment())\r
- {\r
- int max = av.alignment.getWidth() /\r
- 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
- if (overviewPanel != null)\r
- overviewPanel.setBoxPosition();\r
-\r
- repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Dimension calculateIdWidth()\r
- {\r
- Container c = new Container();\r
-\r
- FontMetrics fm = c.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
- id = s.getDisplayId(av.getShowJVSuffix());\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 = c.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
- if (!av.wrapAlignment)\r
- {\r
- annotationSpaceFillerHolder.setVisible(b);\r
- annotationScroller.setVisible(b);\r
- }\r
- repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param wrap DOCUMENT ME!\r
- */\r
- public void setWrapAlignment(boolean wrap)\r
- {\r
- av.startSeq = 0;\r
- scalePanelHolder.setVisible(!wrap);\r
- hscroll.setVisible(!wrap);\r
- idwidthAdjuster.setVisible(!wrap);\r
-\r
- if (wrap)\r
- {\r
- annotationScroller.setVisible(false);\r
- annotationSpaceFillerHolder.setVisible(false);\r
- }\r
- else if (av.showAnnotation)\r
- {\r
- annotationScroller.setVisible(true);\r
- annotationSpaceFillerHolder.setVisible(true);\r
- }\r
-\r
- idSpaceFillerPanel1.setVisible(!wrap);\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
- return true;\r
- }\r
-\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
- 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
- if ( (hextent + x) > av.getAlignment().getWidth())\r
- {\r
- x = av.getAlignment().getWidth() - hextent;\r
- }\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
- if (x < 0)\r
- {\r
- x = 0;\r
- }\r
-\r
- hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());\r
- vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void adjustmentValueChanged(AdjustmentEvent evt)\r
- {\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
- if (evt.getSource() == vscroll)\r
- {\r
- int offy = vscroll.getValue();\r
-\r
- if (av.getWrapAlignment())\r
- {\r
- int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.\r
- 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
- if (overviewPanel != null)\r
- {\r
- overviewPanel.setBoxPosition();\r
- }\r
-\r
- int xShift = av.getStartRes() - oldX;\r
- int yShift = av.getStartSeq() - oldY;\r
-\r
- if ( (xShift != 0 && yShift != 0) ||\r
- (Math.abs(xShift) > av.getEndRes() - av.getStartRes()\r
- || Math.abs(yShift) > av.getEndSeq() - av.getStartSeq())\r
- || av.getWrapAlignment()\r
- || !fastPaint)\r
- {\r
- // Either no shift at all, or shift greater than visible amount\r
- repaint();\r
- }\r
- else\r
- {\r
- idPanel.idCanvas.fastPaint(yShift);\r
- seqPanel.seqCanvas.fastPaint(xShift, yShift);\r
-\r
- scalePanel.repaint();\r
-\r
- if (av.getShowAnnotation())\r
- {\r
- annotationPanel.fastPaint(xShift);\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param g DOCUMENT ME!\r
- */\r
- public void paintComponent(Graphics g)\r
- {\r
- invalidate();\r
-\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() /\r
- seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) +1;\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
- if( this.getVisibleRect().getBounds() == g.getClipBounds() )\r
- {\r
- if (overviewPanel != null)\r
- overviewPanel.updateOverviewImage();\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
- 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
- /**\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 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.adjustPanelHeight() + 3;\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).getDisplayId\r
- ( av.getShowJVSuffix());\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 + 3);\r
- alabels.drawComponent( (Graphics2D) pg, idWidth);\r
- pg.translate(idWidth, 0);\r
- annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +\r
- 1);\r
- }\r
-\r
- return Printable.PAGE_EXISTS;\r
- }\r
-\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)\r
- throws PrinterException\r
- {\r
-\r
- int annotationHeight = 0;\r
- AnnotationLabels labels = null;\r
- if (av.showAnnotation)\r
- {\r
- annotationHeight = annotationPanel.adjustPanelHeight();\r
- labels = new AnnotationLabels(av);\r
- }\r
-\r
- int hgap = av.charHeight;\r
- if (av.scaleAboveWrapped)\r
- hgap += av.charHeight;\r
-\r
- int cHeight = av.getAlignment().getHeight() * av.charHeight\r
- + hgap\r
- + annotationHeight;\r
-\r
- int idWidth = calculateIdWidth().width + 4;\r
-\r
- int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -\r
- idWidth);\r
-\r
- int totalHeight = cHeight * (av.alignment.getWidth() / resWidth + 1);\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 = hgap;\r
- Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
- av.getFont().getSize());\r
- pg.setFont(italic);\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.getDisplayId( av.getShowJVSuffix());\r
-\r
- pg.drawString(string, 0,\r
- ( (i * av.charHeight) + ypos + av.charHeight) -\r
- (av.charHeight / 5));\r
- }\r
- if (labels != null)\r
- {\r
- pg.translate(0,\r
- ypos +\r
- (av.getAlignment().getHeight() * av.charHeight));\r
-\r
- pg.setFont(av.getFont());\r
- labels.drawComponent(pg, idWidth);\r
- pg.setFont(italic);\r
- pg.translate(0,\r
- -ypos -\r
- (av.getAlignment().getHeight() * av.charHeight));\r
- }\r
-\r
- ypos += cHeight;\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
- }\r
- else\r
- {\r
- return Printable.NO_SUCH_PAGE;\r
- }\r
- }\r
-\r
- void makeAlignmentImage(int type, File file)\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
- height = getWrappedHeight();\r
- width = seqPanel.getWidth() + idPanel.getWidth();\r
- }\r
- else if (av.getShowAnnotation())\r
- {\r
- height += annotationPanel.adjustPanelHeight() + 3;\r
- }\r
-\r
- jalview.util.ImageMaker im;\r
- if(type==jalview.util.ImageMaker.PNG)\r
- im = new jalview.util.ImageMaker(this,\r
- jalview.util.ImageMaker.PNG,\r
- "Create PNG image from alignment",\r
- width, height, file, null);\r
- else\r
- im = new jalview.util.ImageMaker(this,\r
- jalview.util.ImageMaker.EPS,\r
- "Create EPS file from alignment",\r
- width, height, file, alignFrame.getTitle() );\r
-\r
- try\r
- {\r
- if (av.getWrapAlignment())\r
- {\r
- if(im.getGraphics()!=null)\r
- printWrappedAlignment(im.getGraphics(), width, height, 0);\r
- }\r
- else\r
- {\r
- if(im.getGraphics()!=null)\r
- printUnwrapped(im.getGraphics(), width, height, 0);\r
- }\r
-\r
- im.writeImage();\r
- }\r
- catch (OutOfMemoryError err)\r
- {\r
- System.out.println("########################\n"\r
- + "OUT OF MEMORY " + file + "\n"\r
- + "########################");\r
-\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "Out of Memory Creating Image!!"\r
- +\r
- "\nSee help files for increasing Java Virtual Machine memory."\r
- , "Out of memory",\r
- JOptionPane.WARNING_MESSAGE);\r
- System.out.println("Create IMAGE: " + err);\r
- System.gc();\r
-\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void makeEPS(File epsFile)\r
- {\r
- makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void makePNG(File pngFile)\r
- {\r
- makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);\r
- }\r
-\r
- public void makePNGImageMap(File imgMapFile, String imageName)\r
- {\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
- int getWrappedHeight()\r
- {\r
-\r
- int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(\r
- seqPanel.seqCanvas.getWidth());\r
-\r
- int hgap = av.charHeight;\r
- if (av.scaleAboveWrapped)\r
- hgap += av.charHeight;\r
-\r
- int annotationHeight = 0;\r
- if (av.showAnnotation)\r
- {\r
- annotationHeight = annotationPanel.adjustPanelHeight();\r
- }\r
-\r
- int cHeight = av.getAlignment().getHeight() * av.charHeight\r
- + hgap\r
- + annotationHeight;\r
-\r
- int height = ( (av.alignment.getWidth() / chunkWidth) + 1) * cHeight;\r
-\r
- return height;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
- class Preview\r
- 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
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
- class PreviewPanel\r
- 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
-}\r
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.analysis.AnnotationSorter;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.SequenceRenderer;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.ImageExporter.ImageWriterI;
+import jalview.io.HTMLOutput;
+import jalview.jbgui.GAlignmentPanel;
+import jalview.math.AlignmentDimension;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.Comparison;
+import jalview.util.ImageMaker;
+import jalview.util.MessageManager;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.image.BufferedImage;
+import java.awt.print.PageFormat;
+import java.awt.print.Printable;
+import java.awt.print.PrinterException;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.PrintWriter;
+import java.util.List;
+
+import javax.swing.SwingUtilities;
+
+/**
+ * The main panel of an AlignFrame, containing holders for the IdPanel,
+ * SeqPanel, AnnotationLabels (a JPanel), and AnnotationPanel.
+ *
+ * Additional holders contain an IdPanelWidthAdjuster space above the idPanel,
+ * AnnotationScroller (JScrollPane for AnnotationPanel), and vertical and
+ * horizontal scrollbars.
+ *
+ *
+ *
+ * @author $author$
+ * @version $Revision: 1.161 $
+ */
+@SuppressWarnings("serial")
+public class AlignmentPanel extends GAlignmentPanel implements
+ AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI
+{
+ public AlignViewport av;
+
+ OverviewPanel overviewPanel;
+
+ private SeqPanel seqPanel;
+
+ private IdPanel idPanel;
+
+ IdwidthAdjuster idwidthAdjuster;
+
+ public AlignFrame alignFrame;
+
+ private ScalePanel scalePanel;
+
+ private AnnotationPanel annotationPanel;
+
+ private AnnotationLabels alabels;
+
+ private int hextent = 0;
+
+ private int vextent = 0;
+
+ /*
+ * Flag set while scrolling to follow complementary cDNA/protein scroll. When
+ * false, suppresses invoking the same method recursively.
+ */
+ private boolean scrollComplementaryPanel = true;
+
+ private PropertyChangeListener propertyChangeListener;
+
+ private CalculationChooser calculationDialog;
+
+ /**
+ * Creates a new AlignmentPanel object.
+ *
+ * @param af
+ * @param av
+ */
+ public AlignmentPanel(AlignFrame af, final AlignViewport av)
+ {
+ setBackground(Color.white); // BH 2019
+ setOpaque(true);
+ alignFrame = af;
+ this.av = av;
+ setSeqPanel(new SeqPanel(av, this));
+ setIdPanel(new IdPanel(av, this));
+
+ setScalePanel(new ScalePanel(av, this));
+
+ idPanelHolder.add(getIdPanel(), BorderLayout.CENTER);
+ idwidthAdjuster = new IdwidthAdjuster(this);
+ idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
+
+ setAnnotationPanel(new AnnotationPanel(this));
+ setAlabels(new AnnotationLabels(this));
+
+ annotationScroller.setViewportView(getAnnotationPanel());
+ annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER);
+ if (!av.isShowAnnotation())
+ {
+ annotationScroller.setVisible(false);
+ annotationSpaceFillerHolder.setVisible(false);
+ }
+ scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER);
+ seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER);
+
+ setScrollValues(0, 0);
+
+ hscroll.addAdjustmentListener(this);
+ vscroll.addAdjustmentListener(this);
+
+ addComponentListener(new ComponentAdapter()
+ {
+ @Override
+ public void componentResized(ComponentEvent evt)
+ {
+ // reset the viewport ranges when the alignment panel is resized
+ // in particular, this initialises the end residue value when Jalview
+ // is initialised
+ ViewportRanges ranges = av.getRanges();
+ if (av.getWrapAlignment())
+ {
+ int widthInRes = getSeqPanel().seqCanvas.getWrappedCanvasWidth(
+ getSeqPanel().seqCanvas.getWidth());
+ ranges.setViewportWidth(widthInRes);
+ }
+ else
+ {
+ int widthInRes = getSeqPanel().seqCanvas.getWidth()
+ / av.getCharWidth();
+ int heightInSeq = getSeqPanel().seqCanvas.getHeight()
+ / av.getCharHeight();
+
+ ranges.setViewportWidth(widthInRes);
+ ranges.setViewportHeight(heightInSeq);
+ }
+ }
+
+ });
+
+ final AlignmentPanel ap = this;
+ propertyChangeListener = new PropertyChangeListener()
+ {
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ if (evt.getPropertyName().equals("alignment"))
+ {
+ PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
+ alignmentChanged();
+ }
+ }
+ };
+ av.addPropertyChangeListener(propertyChangeListener);
+
+ av.getRanges().addPropertyChangeListener(this);
+ fontChanged();
+ adjustAnnotationHeight();
+ updateLayout();
+ }
+
+ @Override
+ public AlignViewportI getAlignViewport()
+ {
+ return av;
+ }
+
+ public void alignmentChanged()
+ {
+ av.alignmentChanged(this);
+
+ if (getCalculationDialog() != null)
+ {
+ getCalculationDialog().validateCalcTypes();
+ }
+
+ alignFrame.updateEditMenuBar();
+
+ // no idea if we need to update structure
+ paintAlignment(true, true);
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void fontChanged()
+ {
+ // set idCanvas bufferedImage to null
+ // to prevent drawing old image
+ FontMetrics fm = getFontMetrics(av.getFont());
+
+ scalePanelHolder.setPreferredSize(
+ new Dimension(10, av.getCharHeight() + fm.getDescent()));
+ idSpaceFillerPanel1.setPreferredSize(
+ new Dimension(10, av.getCharHeight() + fm.getDescent()));
+ idwidthAdjuster.invalidate();
+ scalePanelHolder.invalidate();
+ // BH 2018 getIdPanel().getIdCanvas().gg = null;
+ getSeqPanel().seqCanvas.img = null;
+ getAnnotationPanel().adjustPanelHeight();
+
+ Dimension d = calculateIdWidth();
+
+ d.setSize(d.width + 4, d.height);
+ getIdPanel().getIdCanvas().setPreferredSize(d);
+ hscrollFillerPanel.setPreferredSize(d);
+
+ repaint();
+ }
+
+ /**
+ * Calculate the width of the alignment labels based on the displayed names
+ * and any bounds on label width set in preferences.
+ *
+ * @return Dimension giving the maximum width of the alignment label panel
+ * that should be used.
+ */
+ public Dimension calculateIdWidth()
+ {
+ // calculate sensible default width when no preference is available
+ Dimension r = null;
+ if (av.getIdWidth() < 0)
+ {
+ int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
+ int maxwidth = Math.max(20, Math.min(afwidth - 200, 2 * afwidth / 3));
+ r = calculateIdWidth(maxwidth);
+ av.setIdWidth(r.width);
+ }
+ else
+ {
+ r = new Dimension();
+ r.width = av.getIdWidth();
+ r.height = 0;
+ }
+ return r;
+ }
+
+ /**
+ * Calculate the width of the alignment labels based on the displayed names
+ * and any bounds on label width set in preferences.
+ *
+ * @param maxwidth
+ * -1 or maximum width allowed for IdWidth
+ * @return Dimension giving the maximum width of the alignment label panel
+ * that should be used.
+ */
+ public Dimension calculateIdWidth(int maxwidth)
+ {
+ Container c = new Container();
+
+ FontMetrics fm = c.getFontMetrics(
+ new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
+
+ AlignmentI al = av.getAlignment();
+ int i = 0;
+ int idWidth = 0;
+ String id;
+
+ while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
+ {
+ SequenceI s = al.getSequenceAt(i);
+
+ id = s.getDisplayId(av.getShowJVSuffix());
+
+ if (fm.stringWidth(id) > idWidth)
+ {
+ idWidth = fm.stringWidth(id);
+ }
+
+ i++;
+ }
+
+ // Also check annotation label widths
+ i = 0;
+
+ if (al.getAlignmentAnnotation() != null)
+ {
+ fm = c.getFontMetrics(getAlabels().getFont());
+
+ while (i < al.getAlignmentAnnotation().length)
+ {
+ String label = al.getAlignmentAnnotation()[i].label;
+
+ if (fm.stringWidth(label) > idWidth)
+ {
+ idWidth = fm.stringWidth(label);
+ }
+
+ i++;
+ }
+ }
+
+ return new Dimension(
+ maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth), 12);
+ }
+
+ /**
+ * Highlight the given results on the alignment
+ *
+ */
+ public void highlightSearchResults(SearchResultsI results)
+ {
+ boolean scrolled = scrollToPosition(results, 0, false);
+
+ boolean fastPaint = !(scrolled && av.getWrapAlignment());
+
+ getSeqPanel().seqCanvas.highlightSearchResults(results, fastPaint);
+ }
+
+ /**
+ * Scroll the view to show the position of the highlighted region in results
+ * (if any)
+ *
+ * @param searchResults
+ * @return
+ */
+ public boolean scrollToPosition(SearchResultsI searchResults)
+ {
+ return scrollToPosition(searchResults, 0, false);
+ }
+
+ /**
+ * Scrolls the view (if necessary) to show the position of the first
+ * highlighted region in results (if any). Answers true if the view was
+ * scrolled, or false if no matched region was found, or it is already
+ * visible.
+ *
+ * @param results
+ * @param verticalOffset
+ * if greater than zero, allows scrolling to a position below the
+ * first displayed sequence
+ * @param centre
+ * if true, try to centre the search results horizontally in the view
+ * @return
+ */
+ protected boolean scrollToPosition(SearchResultsI results,
+ int verticalOffset, boolean centre)
+ {
+ int startv, endv, starts, ends;
+ ViewportRanges ranges = av.getRanges();
+
+ if (results == null || results.isEmpty() || av == null
+ || av.getAlignment() == null)
+ {
+ return false;
+ }
+ int seqIndex = av.getAlignment().findIndex(results);
+ if (seqIndex == -1)
+ {
+ return false;
+ }
+ SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
+
+ int[] r = results.getResults(seq, 0, av.getAlignment().getWidth());
+ if (r == null)
+ {
+ return false;
+ }
+ int start = r[0];
+ int end = r[1];
+
+ /*
+ * To centre results, scroll to positions half the visible width
+ * left/right of the start/end positions
+ */
+ if (centre)
+ {
+ int offset = (ranges.getEndRes() - ranges.getStartRes() + 1) / 2 - 1;
+ start = Math.max(start - offset, 0);
+ end = end + offset - 1;
+ }
+ if (start < 0)
+ {
+ return false;
+ }
+ if (end == seq.getEnd())
+ {
+ return false;
+ }
+
+ if (av.hasHiddenColumns())
+ {
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ start = hidden.absoluteToVisibleColumn(start);
+ end = hidden.absoluteToVisibleColumn(end);
+ if (start == end)
+ {
+ if (!hidden.isVisible(r[0]))
+ {
+ // don't scroll - position isn't visible
+ return false;
+ }
+ }
+ }
+
+ /*
+ * allow for offset of target sequence (actually scroll to one above it)
+ */
+ seqIndex = Math.max(0, seqIndex - verticalOffset);
+ boolean scrollNeeded = true;
+
+ if (!av.getWrapAlignment())
+ {
+ if ((startv = ranges.getStartRes()) >= start)
+ {
+ /*
+ * Scroll left to make start of search results visible
+ */
+ setScrollValues(start, seqIndex);
+ }
+ else if ((endv = ranges.getEndRes()) <= end)
+ {
+ /*
+ * Scroll right to make end of search results visible
+ */
+ setScrollValues(startv + end - endv, seqIndex);
+ }
+ else if ((starts = ranges.getStartSeq()) > seqIndex)
+ {
+ /*
+ * Scroll up to make start of search results visible
+ */
+ setScrollValues(ranges.getStartRes(), seqIndex);
+ }
+ else if ((ends = ranges.getEndSeq()) <= seqIndex)
+ {
+ /*
+ * Scroll down to make end of search results visible
+ */
+ setScrollValues(ranges.getStartRes(), starts + seqIndex - ends
+ + 1);
+ }
+ /*
+ * Else results are already visible - no need to scroll
+ */
+ scrollNeeded = false;
+ }
+ else
+ {
+ scrollNeeded = ranges.scrollToWrappedVisible(start);
+ }
+
+ paintAlignment(false, false);
+
+ return scrollNeeded;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public OverviewPanel getOverviewPanel()
+ {
+ return overviewPanel;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param op
+ * DOCUMENT ME!
+ */
+ public void setOverviewPanel(OverviewPanel op)
+ {
+ overviewPanel = op;
+ }
+
+ /**
+ *
+ * @param b
+ * Hide or show annotation panel
+ *
+ */
+ public void setAnnotationVisible(boolean b)
+ {
+ if (!av.getWrapAlignment())
+ {
+ annotationSpaceFillerHolder.setVisible(b);
+ annotationScroller.setVisible(b);
+ }
+ repaint();
+ }
+
+ /**
+ * automatically adjust annotation panel height for new annotation whilst
+ * ensuring the alignment is still visible.
+ */
+ @Override
+ public void adjustAnnotationHeight()
+ {
+ // TODO: display vertical annotation scrollbar if necessary
+ // this is called after loading new annotation onto alignment
+ if (alignFrame.getHeight() == 0)
+ {
+ System.out.println("NEEDS FIXING");
+ }
+ validateAnnotationDimensions(true);
+ addNotify();
+ // TODO: many places call this method and also paintAlignment with various
+ // different settings. this means multiple redraws are triggered...
+ paintAlignment(true, av.needToUpdateStructureViews());
+ }
+
+ /**
+ * calculate the annotation dimensions and refresh slider values accordingly.
+ * need to do repaints/notifys afterwards.
+ */
+ protected void validateAnnotationDimensions(boolean adjustPanelHeight)
+ {
+ // BH 2018.04.18 comment: addNotify() is not appropriate here. We
+ // are not changing ancestors, and keyboard action listeners do
+ // not need to be reset. addNotify() is a very expensive operation,
+ // requiring a full re-layout of all parents and children.
+ // Note in JComponent:
+ // This method is called by the toolkit internally and should
+ // not be called directly by programs.
+ // I note that addNotify() is called in several areas of Jalview.
+
+ int annotationHeight = getAnnotationPanel().adjustPanelHeight();
+ annotationHeight = getAnnotationPanel()
+ .adjustForAlignFrame(adjustPanelHeight, annotationHeight);
+
+ hscroll.addNotify();
+ annotationScroller.setPreferredSize(
+ new Dimension(annotationScroller.getWidth(), annotationHeight));
+
+ Dimension e = idPanel.getSize();
+ alabels.setSize(new Dimension(e.width, annotationHeight));
+
+
+ annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+ annotationSpaceFillerHolder.getWidth(), annotationHeight));
+ annotationScroller.validate();
+ annotationScroller.addNotify();
+ }
+
+ /**
+ * update alignment layout for viewport settings
+ *
+ * @param wrap
+ * DOCUMENT ME!
+ */
+ public void updateLayout()
+ {
+ fontChanged(); // fires repaint
+ setAnnotationVisible(av.isShowAnnotation());
+ boolean wrap = av.getWrapAlignment();
+ ViewportRanges ranges = av.getRanges();
+ ranges.setStartSeq(0);
+ scalePanelHolder.setVisible(!wrap);
+ hscroll.setVisible(!wrap);
+ idwidthAdjuster.setVisible(!wrap);
+
+ if (wrap)
+ {
+ annotationScroller.setVisible(false);
+ annotationSpaceFillerHolder.setVisible(false);
+ }
+ else if (av.isShowAnnotation())
+ {
+ annotationScroller.setVisible(true);
+ annotationSpaceFillerHolder.setVisible(true);
+ validateAnnotationDimensions(false);
+ }
+
+ int canvasWidth = getSeqPanel().seqCanvas.getWidth();
+ if (canvasWidth > 0)
+ { // may not yet be laid out
+ if (wrap)
+ {
+ int widthInRes = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(canvasWidth);
+ ranges.setViewportWidth(widthInRes);
+ }
+ else
+ {
+ int widthInRes = (canvasWidth / av.getCharWidth());
+ int heightInSeq = (getSeqPanel().seqCanvas.getHeight()
+ / av.getCharHeight());
+
+ ranges.setViewportWidth(widthInRes);
+ ranges.setViewportHeight(heightInSeq);
+ }
+ }
+
+ idSpaceFillerPanel1.setVisible(!wrap);
+
+ repaint();
+ }
+
+ /**
+ * Adjust row/column scrollers to show a visible position in the alignment.
+ *
+ * @param x
+ * visible column to scroll to
+ * @param y
+ * visible row to scroll to
+ *
+ */
+ public void setScrollValues(int xpos, int ypos)
+ {
+ int x = xpos;
+ int y = ypos;
+
+ if (av == null || av.getAlignment() == null)
+ {
+ return;
+ }
+
+ if (av.getWrapAlignment())
+ {
+ setScrollingForWrappedPanel(x);
+ }
+ else
+ {
+ int width = av.getAlignment().getVisibleWidth();
+ int height = av.getAlignment().getHeight();
+
+ hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
+ vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
+
+ if (hextent > width)
+ {
+ hextent = width;
+ }
+
+ if (vextent > height)
+ {
+ vextent = height;
+ }
+
+ if ((hextent + x) > width)
+ {
+ x = width - hextent;
+ }
+
+ if ((vextent + y) > height)
+ {
+ y = height - vextent;
+ }
+
+ if (y < 0)
+ {
+ y = 0;
+ }
+
+ if (x < 0)
+ {
+ x = 0;
+ }
+
+ // update the scroll values
+ hscroll.setValues(x, hextent, 0, width);
+ vscroll.setValues(y, vextent, 0, height);
+ }
+ }
+
+ /**
+ * Respond to adjustment event when horizontal or vertical scrollbar is
+ * changed
+ *
+ * @param evt
+ * adjustment event encoding whether hscroll or vscroll changed
+ */
+ @Override
+ public void adjustmentValueChanged(AdjustmentEvent evt)
+ {
+ if (av.getWrapAlignment())
+ {
+ adjustScrollingWrapped(evt);
+ return;
+ }
+
+ ViewportRanges ranges = av.getRanges();
+
+ if (evt.getSource() == hscroll)
+ {
+ int oldX = ranges.getStartRes();
+ int oldwidth = ranges.getViewportWidth();
+ int x = hscroll.getValue();
+ int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
+
+ // if we're scrolling to the position we're already at, stop
+ // this prevents infinite recursion of events when the scroll/viewport
+ // ranges values are the same
+ if ((x == oldX) && (width == oldwidth))
+ {
+ return;
+ }
+ ranges.setViewportStartAndWidth(x, width);
+ }
+ else if (evt.getSource() == vscroll)
+ {
+ int oldY = ranges.getStartSeq();
+ int oldheight = ranges.getViewportHeight();
+ int y = vscroll.getValue();
+ int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
+
+ // if we're scrolling to the position we're already at, stop
+ // this prevents infinite recursion of events when the scroll/viewport
+ // ranges values are the same
+ if ((y == oldY) && (height == oldheight))
+ {
+ return;
+ }
+ ranges.setViewportStartAndHeight(y, height);
+ }
+ repaint();
+ }
+
+ /**
+ * Responds to a scroll change by setting the start position of the viewport.
+ * Does
+ *
+ * @param evt
+ */
+ protected void adjustScrollingWrapped(AdjustmentEvent evt)
+ {
+ if (evt.getSource() == hscroll)
+ {
+ return; // no horizontal scroll when wrapped
+ }
+ final ViewportRanges ranges = av.getRanges();
+
+ if (evt.getSource() == vscroll)
+ {
+ int newY = vscroll.getValue();
+
+ /*
+ * if we're scrolling to the position we're already at, stop
+ * this prevents infinite recursion of events when the scroll/viewport
+ * ranges values are the same
+ */
+ int oldX = ranges.getStartRes();
+ int oldY = ranges.getWrappedScrollPosition(oldX);
+ if (oldY == newY)
+ {
+ return;
+ }
+ if (newY > -1)
+ {
+ /*
+ * limit page up/down to one width's worth of positions
+ */
+ int rowSize = ranges.getViewportWidth();
+ int newX = newY > oldY ? oldX + rowSize : oldX - rowSize;
+ ranges.setViewportStartAndWidth(Math.max(0, newX), rowSize);
+ }
+ }
+ else
+ {
+ // This is only called if file loaded is a jar file that
+ // was wrapped when saved and user has wrap alignment true
+ // as preference setting
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ // When updating scrolling to use ViewportChange events, this code
+ // could not be validated and it is not clear if it is now being
+ // called. Log warning here in case it is called and unforeseen
+ // problems occur
+ Cache.log.warn(
+ "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
+
+ // scroll to start of panel
+ ranges.setStartRes(0);
+ ranges.setStartSeq(0);
+ }
+ });
+ }
+ repaint();
+ }
+
+ /* (non-Javadoc)
+ * @see jalview.api.AlignmentViewPanel#paintAlignment(boolean)
+ */
+ @Override
+ public void paintAlignment(boolean updateOverview,
+ boolean updateStructures)
+ {
+ final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
+ av.isShowAutocalculatedAbove());
+ sorter.sort(getAlignment().getAlignmentAnnotation(),
+ av.getSortAnnotationsBy());
+ repaint();
+
+ if (updateStructures)
+ {
+ av.getStructureSelectionManager().sequenceColoursChanged(this);
+ }
+ if (updateOverview)
+ {
+
+ if (overviewPanel != null)
+ {
+ overviewPanel.updateOverviewImage();
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ */
+ @Override
+ public void paintComponent(Graphics g)
+ {
+
+ invalidate(); // needed so that the id width adjuster works correctly
+
+ Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
+ idPanelHolder.setPreferredSize(d);
+ hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
+
+ validate(); // needed so that the id width adjuster works correctly
+
+ /*
+ * set scroll bar positions - tried to remove but necessary for split panel to resize correctly
+ * though I still think this call should be elsewhere.
+ */
+ ViewportRanges ranges = av.getRanges();
+ setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
+ super.paintComponent(g);
+ }
+
+ /**
+ * Set vertical scroll bar position, and number of increments, for wrapped
+ * panel
+ *
+ * @param topLeftColumn
+ * the column position at top left (0..)
+ */
+ private void setScrollingForWrappedPanel(int topLeftColumn)
+ {
+ ViewportRanges ranges = av.getRanges();
+ int scrollPosition = ranges.getWrappedScrollPosition(topLeftColumn);
+ int maxScroll = ranges.getWrappedMaxScroll(topLeftColumn);
+
+ /*
+ * a scrollbar's value can be set to at most (maximum-extent)
+ * so we add extent (1) to the maxScroll value
+ */
+ vscroll.setUnitIncrement(1);
+ vscroll.setValues(scrollPosition, 1, 0, maxScroll + 1);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pg
+ * DOCUMENT ME!
+ * @param pf
+ * DOCUMENT ME!
+ * @param pi
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws PrinterException
+ * DOCUMENT ME!
+ */
+ @Override
+ public int print(Graphics pg, PageFormat pf, int pi)
+ throws PrinterException
+ {
+ pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
+
+ int pwidth = (int) pf.getImageableWidth();
+ int pheight = (int) pf.getImageableHeight();
+
+ if (av.getWrapAlignment())
+ {
+ return printWrappedAlignment(pwidth, pheight, pi, pg);
+ }
+ else
+ {
+ return printUnwrapped(pwidth, pheight, pi, pg, pg);
+ }
+ }
+
+ /**
+ * Draws the alignment image, including sequence ids, sequences, and
+ * annotation labels and annotations if shown, on either one or two Graphics
+ * contexts.
+ *
+ * @param pageWidth
+ * in pixels
+ * @param pageHeight
+ * in pixels
+ * @param pageIndex
+ * (0, 1, ...)
+ * @param idGraphics
+ * the graphics context for sequence ids and annotation labels
+ * @param alignmentGraphics
+ * the graphics context for sequences and annotations (may or may not
+ * be the same context as idGraphics)
+ * @return
+ * @throws PrinterException
+ */
+ public int printUnwrapped(int pageWidth, int pageHeight, int pageIndex,
+ Graphics idGraphics, Graphics alignmentGraphics)
+ throws PrinterException
+ {
+ final int idWidth = getVisibleIdWidth(false);
+
+ /*
+ * Get the horizontal offset to where we draw the sequences.
+ * This is idWidth if using a single Graphics context, else zero.
+ */
+ final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0
+ : idWidth;
+
+ FontMetrics fm = getFontMetrics(av.getFont());
+ final int charHeight = av.getCharHeight();
+ final int scaleHeight = charHeight + fm.getDescent();
+
+ idGraphics.setColor(Color.white);
+ idGraphics.fillRect(0, 0, pageWidth, pageHeight);
+ idGraphics.setFont(av.getFont());
+
+ /*
+ * How many sequences and residues can we fit on a printable page?
+ */
+ final int totalRes = (pageWidth - idWidth) / av.getCharWidth();
+
+ final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
+
+ final int alignmentWidth = av.getAlignment().getVisibleWidth();
+ int pagesWide = (alignmentWidth / totalRes) + 1;
+
+ final int startRes = (pageIndex % pagesWide) * totalRes;
+ final int endRes = Math.min(startRes + totalRes - 1,
+ alignmentWidth - 1);
+
+ final int startSeq = (pageIndex / pagesWide) * totalSeq;
+ final int alignmentHeight = av.getAlignment().getHeight();
+ final int endSeq = Math.min(startSeq + totalSeq, alignmentHeight);
+
+ int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight;
+
+ if (av.isShowAnnotation())
+ {
+ pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
+ }
+
+ pagesHigh /= pageHeight;
+
+ if (pageIndex >= (pagesWide * pagesHigh))
+ {
+ return Printable.NO_SUCH_PAGE;
+ }
+ final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + 3;
+
+ /*
+ * draw the Scale at horizontal offset, then reset to top left (0, 0)
+ */
+ alignmentGraphics.translate(alignmentGraphicsOffset, 0);
+ getScalePanel().drawScale(alignmentGraphics, startRes, endRes,
+ pageWidth - idWidth, scaleHeight);
+ alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
+
+ /*
+ * Draw the sequence ids, offset for scale height,
+ * then reset to top left (0, 0)
+ */
+ idGraphics.translate(0, scaleHeight);
+ IdCanvas idCanvas = getIdPanel().getIdCanvas();
+ List<SequenceI> selection = av.getSelectionGroup() == null ? null
+ : av.getSelectionGroup().getSequences(null);
+ idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1,
+ selection);
+
+ idGraphics.setFont(av.getFont());
+ idGraphics.translate(0, -scaleHeight);
+
+ /*
+ * draw the sequences, offset for scale height, and id width (if using a
+ * single graphics context), then reset to (0, scale height)
+ */
+ alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
+ getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes,
+ endRes, startSeq, endSeq - 1);
+ alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
+
+ if (av.isShowAnnotation() && (endSeq == alignmentHeight))
+ {
+ /*
+ * draw annotation labels; drawComponent() translates by
+ * getScrollOffset(), so compensate for that first;
+ * then reset to (0, scale height)
+ */
+ int offset = getAlabels().getScrollOffset();
+ idGraphics.translate(0, -offset);
+ idGraphics.translate(0, alignmentDrawnHeight);
+ getAlabels().drawComponent(idGraphics, idWidth);
+ idGraphics.translate(0, -alignmentDrawnHeight);
+
+ /*
+ * draw the annotations starting at
+ * (idOffset, alignmentHeight) from (0, scaleHeight)
+ */
+ alignmentGraphics.translate(alignmentGraphicsOffset,
+ alignmentDrawnHeight);
+ getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
+ alignmentGraphics, -1, startRes, endRes + 1);
+ }
+
+ return Printable.PAGE_EXISTS;
+ }
+
+ /**
+ * Prints one page of an alignment in wrapped mode. Returns
+ * Printable.PAGE_EXISTS (0) if a page was drawn, or Printable.NO_SUCH_PAGE if
+ * no page could be drawn (page number out of range).
+ *
+ * @param pageWidth
+ * @param pageHeight
+ * @param pageNumber
+ * (0, 1, ...)
+ * @param g
+ *
+ * @return
+ *
+ * @throws PrinterException
+ */
+ public int printWrappedAlignment(int pageWidth, int pageHeight, int pageNumber,
+ Graphics g) throws PrinterException
+ {
+ int annotationHeight = 0;
+ if (av.isShowAnnotation())
+ {
+ annotationHeight = getAnnotationPanel().adjustPanelHeight();
+ }
+
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
+ {
+ hgap += av.getCharHeight();
+ }
+
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
+ + annotationHeight;
+
+ int idWidth = getVisibleIdWidth(false);
+
+ int maxwidth = av.getAlignment().getVisibleWidth();
+
+ int resWidth = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(pageWidth - idWidth);
+
+ int totalHeight = cHeight * (maxwidth / resWidth + 1);
+
+ g.setColor(Color.white);
+ g.fillRect(0, 0, pageWidth, pageHeight);
+ g.setFont(av.getFont());
+ g.setColor(Color.black);
+
+ /*
+ * method: print the whole wrapped alignment, but with a clip region that
+ * is restricted to the requested page; this supports selective print of
+ * single pages or ranges, (at the cost of some repeated processing in
+ * the 'normal' case, when all pages are printed)
+ */
+ g.translate(0, -pageNumber * pageHeight);
+
+ g.setClip(0, pageNumber * pageHeight, pageWidth, pageHeight);
+
+ /*
+ * draw sequence ids and annotation labels (if shown)
+ */
+ IdCanvas idCanvas = getIdPanel().getIdCanvas();
+ idCanvas.drawIdsWrapped((Graphics2D) g, av, 0, totalHeight);
+
+ g.translate(idWidth, 0);
+
+ getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, pageWidth - idWidth,
+ totalHeight, 0);
+
+ if ((pageNumber * pageHeight) < totalHeight)
+ {
+ return Printable.PAGE_EXISTS;
+ }
+ else
+ {
+ return Printable.NO_SUCH_PAGE;
+ }
+ }
+
+ /**
+ * get current sequence ID panel width, or nominal value if panel were to be
+ * displayed using default settings
+ *
+ * @return
+ */
+ public int getVisibleIdWidth()
+ {
+ return getVisibleIdWidth(true);
+ }
+
+ /**
+ * get current sequence ID panel width, or nominal value if panel were to be
+ * displayed using default settings
+ *
+ * @param onscreen
+ * indicate if the Id width for onscreen or offscreen display should
+ * be returned
+ * @return
+ */
+ public int getVisibleIdWidth(boolean onscreen)
+ {
+ // see if rendering offscreen - check preferences and calc width accordingly
+ if (!onscreen && Cache.getDefault(Preferences.FIGURE_AUTOIDWIDTH, false))
+ {
+ return calculateIdWidth(-1).width + 4;
+ }
+ Integer idwidth = null;
+ if (onscreen || (idwidth = Cache
+ .getIntegerProperty(Preferences.FIGURE_FIXEDIDWIDTH)) == null)
+ {
+ int w = getIdPanel().getWidth();
+ return (w > 0 ? w : calculateIdWidth().width + 4);
+ }
+ return idwidth.intValue() + 4;
+ }
+
+ /**
+ * Builds an image of the alignment of the specified type (EPS/PNG/SVG) and
+ * writes it to the specified file
+ *
+ * @param type
+ * @param file
+ */
+ void makeAlignmentImage(ImageMaker.TYPE type, File file)
+ {
+ final int borderBottomOffset = 5;
+
+ AlignmentDimension aDimension = getAlignmentDimension();
+ // todo use a lambda function in place of callback here?
+ ImageWriterI writer = new ImageWriterI()
+ {
+ @Override
+ public void exportImage(Graphics graphics) throws Exception
+ {
+ if (av.getWrapAlignment())
+ {
+ printWrappedAlignment(aDimension.getWidth(),
+ aDimension.getHeight() + borderBottomOffset, 0, graphics);
+ }
+ else
+ {
+ printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
+ graphics, graphics);
+ }
+ }
+ };
+
+ String fileTitle = alignFrame.getTitle();
+ ImageExporter exporter = new ImageExporter(writer, alignFrame, type,
+ fileTitle);
+ int imageWidth = aDimension.getWidth();
+ int imageHeight = aDimension.getHeight() + borderBottomOffset;
+ String of = MessageManager.getString("label.alignment");
+ exporter.doExport(file, this, imageWidth, imageHeight, of);
+ }
+
+ /**
+ * Calculates and returns a suitable width and height (in pixels) for an
+ * exported image
+ *
+ * @return
+ */
+ public AlignmentDimension getAlignmentDimension()
+ {
+ int maxwidth = av.getAlignment().getVisibleWidth();
+
+ int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
+ + getScalePanel().getHeight();
+ int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
+
+ if (av.getWrapAlignment())
+ {
+ height = getWrappedHeight();
+ if (Jalview.isHeadlessMode())
+ {
+ // need to obtain default alignment width and then add in any
+ // additional allowance for id margin
+ // this duplicates the calculation in getWrappedHeight but adjusts for
+ // offscreen idWith
+ width = alignFrame.getWidth() - vscroll.getPreferredSize().width
+ - alignFrame.getInsets().left - alignFrame.getInsets().right
+ - getVisibleIdWidth() + getVisibleIdWidth(false);
+ }
+ else
+ {
+ width = getSeqPanel().getWidth() + getVisibleIdWidth(false);
+ }
+
+ }
+ else if (av.isShowAnnotation())
+ {
+ height += getAnnotationPanel().adjustPanelHeight() + 3;
+ }
+ return new AlignmentDimension(width, height);
+
+ }
+
+ public void makePNGImageMap(File imgMapFile, String imageName)
+ {
+ // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
+ // ////////////////////////////////////////////
+ int idWidth = getVisibleIdWidth(false);
+ FontMetrics fm = getFontMetrics(av.getFont());
+ int scaleHeight = av.getCharHeight() + fm.getDescent();
+
+ // Gen image map
+ // ////////////////////////////////
+ if (imgMapFile != null)
+ {
+ try
+ {
+ int sSize = av.getAlignment().getHeight();
+ int alwidth = av.getAlignment().getWidth();
+ PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
+ out.println(HTMLOutput.getImageMapHTML());
+ out.println("<img src=\"" + imageName
+ + "\" border=\"0\" usemap=\"#Map\" >"
+ + "<map name=\"Map\">");
+
+ for (int s = 0; s < sSize; s++)
+ {
+ int sy = s * av.getCharHeight() + scaleHeight;
+
+ SequenceI seq = av.getAlignment().getSequenceAt(s);
+ SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
+ for (int column = 0; column < alwidth; column++)
+ {
+ StringBuilder text = new StringBuilder(512);
+ String triplet = null;
+ if (av.getAlignment().isNucleotide())
+ {
+ triplet = ResidueProperties.nucleotideName.get(seq
+ .getCharAt(column) + "");
+ }
+ else
+ {
+ triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(column)
+ + "");
+ }
+
+ if (triplet == null)
+ {
+ continue;
+ }
+
+ int seqPos = seq.findPosition(column);
+ int gSize = groups.length;
+ for (int g = 0; g < gSize; g++)
+ {
+ if (text.length() < 1)
+ {
+ text.append("<area shape=\"rect\" coords=\"")
+ .append((idWidth + column * av.getCharWidth()))
+ .append(",").append(sy).append(",")
+ .append((idWidth + (column + 1) * av.getCharWidth()))
+ .append(",").append((av.getCharHeight() + sy))
+ .append("\"").append(" onMouseOver=\"toolTip('")
+ .append(seqPos).append(" ").append(triplet);
+ }
+
+ if (groups[g].getStartRes() < column
+ && groups[g].getEndRes() > column)
+ {
+ text.append("<br><em>").append(groups[g].getName())
+ .append("</em>");
+ }
+ }
+
+ if (text.length() < 1)
+ {
+ text.append("<area shape=\"rect\" coords=\"")
+ .append((idWidth + column * av.getCharWidth()))
+ .append(",").append(sy).append(",")
+ .append((idWidth + (column + 1) * av.getCharWidth()))
+ .append(",").append((av.getCharHeight() + sy))
+ .append("\"").append(" onMouseOver=\"toolTip('")
+ .append(seqPos).append(" ").append(triplet);
+ }
+ if (!Comparison.isGap(seq.getCharAt(column)))
+ {
+ List<SequenceFeature> features = seq.findFeatures(column, column);
+ for (SequenceFeature sf : features)
+ {
+ if (sf.isContactFeature())
+ {
+ text.append("<br>").append(sf.getType()).append(" ")
+ .append(sf.getBegin()).append(":")
+ .append(sf.getEnd());
+ }
+ else
+ {
+ text.append("<br>");
+ text.append(sf.getType());
+ String description = sf.getDescription();
+ if (description != null
+ && !sf.getType().equals(description))
+ {
+ description = description.replace("\"", """);
+ text.append(" ").append(description);
+ }
+ }
+ String status = sf.getStatus();
+ if (status != null && !"".equals(status))
+ {
+ text.append(" (").append(status).append(")");
+ }
+ }
+ if (text.length() > 1)
+ {
+ text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
+ out.println(text.toString());
+ }
+ }
+ }
+ }
+ out.println("</map></body></html>");
+ out.close();
+
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ } // /////////END OF IMAGE MAP
+
+ }
+
+ int getWrappedHeight()
+ {
+ int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
+
+ if (Jalview.isHeadlessMode())
+ {
+ seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
+ - vscroll.getPreferredSize().width
+ - alignFrame.getInsets().left - alignFrame.getInsets().right;
+ }
+
+ int chunkWidth = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(seqPanelWidth);
+
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
+ {
+ hgap += av.getCharHeight();
+ }
+
+ int annotationHeight = 0;
+ if (av.isShowAnnotation())
+ {
+ annotationHeight = getAnnotationPanel().adjustPanelHeight();
+ }
+
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
+ + annotationHeight;
+
+ int maxwidth = av.getAlignment().getWidth();
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .absoluteToVisibleColumn(maxwidth) - 1;
+ }
+
+ int height = ((maxwidth / chunkWidth) + 1) * cHeight;
+
+ return height;
+ }
+
+ /**
+ * close the panel - deregisters all listeners and nulls any references to
+ * alignment data.
+ */
+ public void closePanel()
+ {
+ PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
+ PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
+ PaintRefresher.RemoveComponent(this);
+
+ closeChildFrames();
+
+ /*
+ * try to ensure references are nulled
+ */
+ if (annotationPanel != null)
+ {
+ annotationPanel.dispose();
+ annotationPanel = null;
+ }
+
+ if (av != null)
+ {
+ av.removePropertyChangeListener(propertyChangeListener);
+ propertyChangeListener = null;
+ StructureSelectionManager ssm = av.getStructureSelectionManager();
+ ssm.removeStructureViewerListener(getSeqPanel(), null);
+ ssm.removeSelectionListener(getSeqPanel());
+ ssm.removeCommandListener(av);
+ ssm.removeStructureViewerListener(getSeqPanel(), null);
+ ssm.removeSelectionListener(getSeqPanel());
+ av.dispose();
+ av = null;
+ }
+ else
+ {
+ if (Cache.log.isDebugEnabled())
+ {
+ Cache.log.warn("Closing alignment panel which is already closed.");
+ }
+ }
+ }
+
+ /**
+ * Close any open dialogs that would be orphaned when this one is closed
+ */
+ protected void closeChildFrames()
+ {
+ if (overviewPanel != null)
+ {
+ overviewPanel.dispose();
+ overviewPanel = null;
+ }
+ if (calculationDialog != null)
+ {
+ calculationDialog.closeFrame();
+ calculationDialog = null;
+ }
+ }
+
+ /**
+ * hides or shows dynamic annotation rows based on groups and av state flags
+ */
+ public void updateAnnotation()
+ {
+ updateAnnotation(false, false);
+ }
+
+ public void updateAnnotation(boolean applyGlobalSettings)
+ {
+ updateAnnotation(applyGlobalSettings, false);
+ }
+
+ public void updateAnnotation(boolean applyGlobalSettings,
+ boolean preserveNewGroupSettings)
+ {
+ av.updateGroupAnnotationSettings(applyGlobalSettings,
+ preserveNewGroupSettings);
+ adjustAnnotationHeight();
+ }
+
+ @Override
+ public AlignmentI getAlignment()
+ {
+ return av == null ? null : av.getAlignment();
+ }
+
+ @Override
+ public String getViewName()
+ {
+ return av.getViewName();
+ }
+
+ /**
+ * Make/Unmake this alignment panel the current input focus
+ *
+ * @param b
+ */
+ public void setSelected(boolean b)
+ {
+ try
+ {
+ if (alignFrame.getSplitViewContainer() != null)
+ {
+ /*
+ * bring enclosing SplitFrame to front first if there is one
+ */
+ ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b);
+ }
+ alignFrame.setSelected(b);
+ } catch (Exception ex)
+ {
+ }
+
+ if (b)
+ {
+ alignFrame.setDisplayedView(this);
+ }
+ }
+
+ @Override
+ public StructureSelectionManager getStructureSelectionManager()
+ {
+ return av.getStructureSelectionManager();
+ }
+
+ @Override
+ public void raiseOOMWarning(String string, OutOfMemoryError error)
+ {
+ new OOMWarning(string, error, this);
+ }
+
+ @Override
+ public jalview.api.FeatureRenderer cloneFeatureRenderer()
+ {
+
+ return new FeatureRenderer(this);
+ }
+
+ @Override
+ public jalview.api.FeatureRenderer getFeatureRenderer()
+ {
+ return seqPanel.seqCanvas.getFeatureRenderer();
+ }
+
+ public void updateFeatureRenderer(
+ jalview.renderer.seqfeatures.FeatureRenderer fr)
+ {
+ fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
+ }
+
+ public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr)
+ {
+ if (getSeqPanel().seqCanvas.getFeatureRenderer() != null)
+ {
+ getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr);
+ }
+ }
+
+ public ScalePanel getScalePanel()
+ {
+ return scalePanel;
+ }
+
+ public void setScalePanel(ScalePanel scalePanel)
+ {
+ this.scalePanel = scalePanel;
+ }
+
+ public SeqPanel getSeqPanel()
+ {
+ return seqPanel;
+ }
+
+ public void setSeqPanel(SeqPanel seqPanel)
+ {
+ this.seqPanel = seqPanel;
+ }
+
+ public AnnotationPanel getAnnotationPanel()
+ {
+ return annotationPanel;
+ }
+
+ public void setAnnotationPanel(AnnotationPanel annotationPanel)
+ {
+ this.annotationPanel = annotationPanel;
+ }
+
+ public AnnotationLabels getAlabels()
+ {
+ return alabels;
+ }
+
+ public void setAlabels(AnnotationLabels alabels)
+ {
+ this.alabels = alabels;
+ }
+
+ public IdPanel getIdPanel()
+ {
+ return idPanel;
+ }
+
+ public void setIdPanel(IdPanel idPanel)
+ {
+ this.idPanel = idPanel;
+ }
+
+ /**
+ * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
+ * The aim is to keep the two alignments 'lined up' on their centre columns.
+ *
+ * @param sr
+ * holds mapped region(s) of this alignment that we are scrolling
+ * 'to'; may be modified for sequence offset by this method
+ * @param verticalOffset
+ * the number of visible sequences to show above the mapped region
+ */
+ protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
+ {
+ scrollToPosition(sr, verticalOffset, true);
+ }
+
+ /**
+ * Set a flag to say do not scroll any (cDNA/protein) complement.
+ *
+ * @param b
+ */
+ protected void setToScrollComplementPanel(boolean b)
+ {
+ this.scrollComplementaryPanel = b;
+ }
+
+ /**
+ * Get whether to scroll complement panel
+ *
+ * @return true if cDNA/protein complement panels should be scrolled
+ */
+ protected boolean isSetToScrollComplementPanel()
+ {
+ return this.scrollComplementaryPanel;
+ }
+
+ /**
+ * Redraw sensibly.
+ *
+ * @adjustHeight if true, try to recalculate panel height for visible
+ * annotations
+ */
+ protected void refresh(boolean adjustHeight)
+ {
+ validateAnnotationDimensions(adjustHeight);
+ addNotify();
+ if (adjustHeight)
+ {
+ // sort, repaint, update overview
+ paintAlignment(true, false);
+ }
+ else
+ {
+ // lightweight repaint
+ repaint();
+ }
+ }
+
+ @Override
+ /**
+ * Property change event fired when a change is made to the viewport ranges
+ * object associated with this alignment panel's viewport
+ */
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ // update this panel's scroll values based on the new viewport ranges values
+ ViewportRanges ranges = av.getRanges();
+ int x = ranges.getStartRes();
+ int y = ranges.getStartSeq();
+ setScrollValues(x, y);
+
+ // now update any complementary alignment (its viewport ranges object
+ // is different so does not get automatically updated)
+ if (isSetToScrollComplementPanel())
+ {
+ setToScrollComplementPanel(false);
+ av.scrollComplementaryAlignment();
+ setToScrollComplementPanel(true);
+ }
+ }
+
+ /**
+ * Set the reference to the PCA/Tree chooser dialog for this panel. This
+ * reference should be nulled when the dialog is closed.
+ *
+ * @param calculationChooser
+ */
+ public void setCalculationDialog(CalculationChooser calculationChooser)
+ {
+ calculationDialog = calculationChooser;
+ }
+
+ /**
+ * Returns the reference to the PCA/Tree chooser dialog for this panel (null
+ * if none is open)
+ */
+ public CalculationChooser getCalculationDialog()
+ {
+ return calculationDialog;
+ }
+
+ @Override
+ public SequenceRenderer getSequenceRenderer()
+ {
+ return seqPanel.seqCanvas.getSequenceRenderer();
+ }
+
+ public boolean scrollTo(int ostart, int end, int seqIndex,
+ boolean scrollToNearest, boolean redrawOverview)
+ {
+ int startv, endv, starts, ends;// , width;
+
+ int start = -1;
+ if (av.hasHiddenColumns())
+ {
+ AlignmentI al = av.getAlignment();
+ start = al.getHiddenColumns().absoluteToVisibleColumn(ostart);
+ end = al.getHiddenColumns().absoluteToVisibleColumn(end);
+ if (start == end)
+ {
+ if (!scrollToNearest && !al.getHiddenColumns().isVisible(ostart))
+ {
+ // don't scroll - position isn't visible
+ return false;
+ }
+ }
+ }
+ else
+ {
+ start = ostart;
+ }
+
+ ViewportRanges ranges = av.getRanges();
+ if (!av.getWrapAlignment())
+ {
+ /*
+ * int spos=av.getStartRes(),sqpos=av.getStartSeq(); if ((startv =
+ * av.getStartRes()) >= start) { spos=start-1; // seqIn //
+ * setScrollValues(start - 1, seqIndex); } else if ((endv =
+ * av.getEndRes()) <= end) { // setScrollValues(spos=startv + 1 + end -
+ * endv, seqIndex); spos=startv + 1 + end - endv; } else if ((starts =
+ * av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(),
+ * seqIndex); } else if ((ends = av.getEndSeq()) <= seqIndex) {
+ * setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); }
+ */
+
+ // below is scrolling logic up to Jalview 2.8.2
+ // if ((av.getStartRes() > end)
+ // || (av.getEndRes() < start)
+ // || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
+ // {
+ // if (start > av.getAlignment().getWidth() - hextent)
+ // {
+ // start = av.getAlignment().getWidth() - hextent;
+ // if (start < 0)
+ // {
+ // start = 0;
+ // }
+ //
+ // }
+ // if (seqIndex > av.getAlignment().getHeight() - vextent)
+ // {
+ // seqIndex = av.getAlignment().getHeight() - vextent;
+ // if (seqIndex < 0)
+ // {
+ // seqIndex = 0;
+ // }
+ // }
+ // setScrollValues(start, seqIndex);
+ // }
+ // logic copied from jalview.gui.AlignmentPanel:
+ if ((startv = ranges.getStartRes()) >= start)
+ {
+ /*
+ * Scroll left to make start of search results visible
+ */
+ setScrollValues(start - 1, seqIndex);
+ }
+ else if ((endv = ranges.getEndRes()) <= end)
+ {
+ /*
+ * Scroll right to make end of search results visible
+ */
+ setScrollValues(startv + 1 + end - endv, seqIndex);
+ }
+ else if ((starts = ranges.getStartSeq()) > seqIndex)
+ {
+ /*
+ * Scroll up to make start of search results visible
+ */
+ setScrollValues(ranges.getStartRes(), seqIndex);
+ }
+ else if ((ends = ranges.getEndSeq()) <= seqIndex)
+ {
+ /*
+ * Scroll down to make end of search results visible
+ */
+ setScrollValues(ranges.getStartRes(), starts + seqIndex - ends + 1);
+ }
+ /*
+ * Else results are already visible - no need to scroll
+ */
+ }
+ else
+ {
+ ranges.scrollToWrappedVisible(start);
+ }
+
+ paintAlignment(redrawOverview, false);
+ return true;
+ }
+
+ @Override
+ public void overviewDone(BufferedImage miniMe)
+ {
+ overviewPanel.canvas.finalizeDraw(miniMe);
+ }
+
+
+ private boolean holdRepaint = false;
+
+ public boolean getHoldRepaint()
+ {
+ return holdRepaint;
+ }
+
+ public void setHoldRepaint(boolean b)
+ {
+ if (holdRepaint == b)
+ {
+ return;
+ }
+ holdRepaint = b;
+ if (!b)
+ {
+ repaint();
+ }
+ }
+
+ @Override
+ public void repaint()
+ {
+ if (holdRepaint)
+ {
+ // System.out.println("AP repaint holding");
+ // Platform.stackTrace();
+ return;
+ }
+ super.repaint();
+ }
+
+}