-/*\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 (idPanel.getWidth() == 0)\r
- {\r
- width += calculateIdWidth().getWidth() + 4;\r
- }\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
- int s, sSize = av.alignment.getHeight(),\r
- res, alwidth = av.alignment.getWidth(), g, gSize, f, fSize, sy;\r
- StringBuffer text = new StringBuffer();\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 (s = 0; s < sSize; s++)\r
- {\r
- sy = s * av.charHeight + scaleHeight;\r
-\r
- SequenceI seq = av.alignment.getSequenceAt(s);\r
- java.util.Vector features = seq.getDatasetSequence().getSequenceFeatures();\r
- SequenceGroup[] groups = av.alignment.findAllGroups(seq);\r
- for(res =0; res<alwidth; res++)\r
- {\r
- text = new StringBuffer();\r
- Object obj = null;\r
- if(av.alignment.isNucleotide())\r
- obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)+"" );\r
- else\r
- obj = ResidueProperties.aa2Triplet.get(\r
- seq.getCharAt(res) + "");\r
-\r
- if (obj == null)\r
- continue;\r
-\r
- String triplet = obj.toString();\r
- int alIndex = seq.findPosition(res);\r
- gSize = groups.length;\r
- for (g = 0; g < gSize; g++)\r
- {\r
- if(text.length()<1)\r
- {\r
- text.append("<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
- }\r
-\r
- if(groups[g].getStartRes()<res && groups[g].getEndRes()>res)\r
- text.append("<br><em>" + groups[g].getName() + "</em>");\r
- }\r
-\r
- if (features != null)\r
- {\r
- if(text.length()<1)\r
- {\r
- text.append("<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
- }\r
- fSize = features.size();\r
- for (f = 0; f < fSize; f++)\r
- {\r
- SequenceFeature sf = (SequenceFeature) features.elementAt(f);\r
-\r
- if ( (sf.getBegin() <= seq.findPosition(res)) &&\r
- (sf.getEnd() >= seq.findPosition(res)))\r
- {\r
- if (sf.getType().equals("disulfide bond"))\r
- {\r
- if (sf.getBegin() == seq.findPosition(res)\r
- || sf.getEnd() == seq.findPosition(res))\r
- {\r
- text.append("<br>disulfide bond " + sf.getBegin() + ":" +\r
- sf.getEnd());\r
- }\r
- }\r
- else\r
- {\r
- text.append("<br>");\r
- text.append(sf.getType());\r
- if (sf.getDescription() != null && !sf.getType().equals(sf.getDescription()))\r
- text.append(" " + sf.getDescription());\r
-\r
- if (sf.getStatus() != null && sf.getStatus().length()>0)\r
- {\r
- text.append(" (" + sf.getStatus() + ")");\r
- }\r
- }\r
- }\r
-\r
- }\r
- }\r
- if(text.length()>1)\r
- {\r
- text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");\r
- out.println(text.toString());\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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+package jalview.gui;
+
+import java.beans.*;
+import java.io.*;
+import java.util.Hashtable;
+import java.util.Vector;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.print.*;
+import javax.swing.*;
+
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.datamodel.*;
+import jalview.jbgui.*;
+import jalview.schemes.*;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision: 1.161 $
+ */
+public class AlignmentPanel extends GAlignmentPanel implements
+ AdjustmentListener, Printable, AlignmentViewPanel
+{
+ public AlignViewport av;
+
+ OverviewPanel overviewPanel;
+
+ SeqPanel seqPanel;
+
+ IdPanel idPanel;
+
+ IdwidthAdjuster idwidthAdjuster;
+
+ /** DOCUMENT ME!! */
+ public AlignFrame alignFrame;
+
+ ScalePanel scalePanel;
+
+ AnnotationPanel annotationPanel;
+
+ AnnotationLabels alabels;
+
+ // this value is set false when selection area being dragged
+ boolean fastPaint = true;
+
+ int hextent = 0;
+
+ int vextent = 0;
+
+ /**
+ * Creates a new AlignmentPanel object.
+ *
+ * @param af
+ * DOCUMENT ME!
+ * @param av
+ * DOCUMENT ME!
+ */
+ public AlignmentPanel(AlignFrame af, final AlignViewport av)
+ {
+ alignFrame = af;
+ this.av = av;
+ seqPanel = new SeqPanel(av, this);
+ idPanel = new IdPanel(av, this);
+
+ scalePanel = new ScalePanel(av, this);
+
+ idPanelHolder.add(idPanel, BorderLayout.CENTER);
+ idwidthAdjuster = new IdwidthAdjuster(this);
+ idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
+
+ annotationPanel = new AnnotationPanel(this);
+ alabels = new AnnotationLabels(this);
+
+ annotationScroller.setViewportView(annotationPanel);
+ annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
+
+ scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
+ seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
+
+ setScrollValues(0, 0);
+
+ setAnnotationVisible(av.getShowAnnotation());
+
+ hscroll.addAdjustmentListener(this);
+ vscroll.addAdjustmentListener(this);
+
+ final AlignmentPanel ap = this;
+ av.addPropertyChangeListener(new PropertyChangeListener()
+ {
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ if (evt.getPropertyName().equals("alignment"))
+ {
+ PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
+ alignmentChanged();
+ }
+ }
+ });
+ fontChanged();
+ adjustAnnotationHeight();
+
+ }
+
+ public void alignmentChanged()
+ {
+ av.alignmentChanged(this);
+
+ alignFrame.updateEditMenuBar();
+
+ paintAlignment(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.charHeight
+ + fm.getDescent()));
+ idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av.charHeight
+ + fm.getDescent()));
+
+ idPanel.idCanvas.gg = null;
+ seqPanel.seqCanvas.img = null;
+ annotationPanel.adjustPanelHeight();
+
+ Dimension d = calculateIdWidth();
+ d.setSize(d.width + 4, d.height);
+ idPanel.idCanvas.setPreferredSize(d);
+ hscrollFillerPanel.setPreferredSize(d);
+
+ if (overviewPanel != null)
+ {
+ overviewPanel.setBoxPosition();
+ }
+
+ 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()
+ {
+ Container c = new Container();
+
+ FontMetrics fm = c.getFontMetrics(new Font(av.font.getName(),
+ Font.ITALIC, av.font.getSize()));
+
+ AlignmentI al = av.getAlignment();
+ int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
+ int maxwidth = Math.max(20,
+ Math.min(afwidth - 200, (int) 2 * afwidth / 3));
+ 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(alabels.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(Math.min(maxwidth, idWidth), 12);
+ }
+
+ /**
+ * Highlight the given results on the alignment.
+ *
+ */
+ public void highlightSearchResults(SearchResults results)
+ {
+ scrollToPosition(results);
+ seqPanel.seqCanvas.highlightSearchResults(results);
+ }
+
+ /**
+ * scroll the view to show the position of the highlighted region in results
+ * (if any) and redraw the overview
+ *
+ * @param results
+ */
+ public boolean scrollToPosition(SearchResults results)
+ {
+ return scrollToPosition(results, true);
+ }
+
+ /**
+ * scroll the view to show the position of the highlighted region in results
+ * (if any)
+ *
+ * @param results
+ * @param redrawOverview
+ * - when set, the overview will be recalculated (takes longer)
+ * @return false if results were not found
+ */
+ public boolean scrollToPosition(SearchResults results,
+ boolean redrawOverview)
+ {
+ int startv, endv, starts, ends, width;
+ // TODO: properly locate search results in view when large numbers of hidden
+ // columns exist before highlighted region
+ // do we need to scroll the panel?
+ // TODO: tons of nullpointereexceptions raised here.
+ if (results != null && results.getSize() > 0 && av != null
+ && av.alignment != null)
+ {
+ int seqIndex = av.alignment.findIndex(results);
+ if (seqIndex == -1)
+ {
+ return false;
+ }
+ SequenceI seq = av.alignment.getSequenceAt(seqIndex);
+
+ int[] r=results.getResults(seq, 0, av.alignment.getWidth());
+ if (r == null)
+ {
+ return false;
+ }
+ int start = r[0];
+ int end = r[1];
+ // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); //
+ // DEBUG
+ if (start < 0)
+ {
+ return false;
+ }
+ if (end == seq.getEnd())
+ {
+ return false;
+ }
+ if (av.hasHiddenColumns)
+ {
+ start = av.getColumnSelection().findColumnPosition(start);
+ end = av.getColumnSelection().findColumnPosition(end);
+ if (start==end)
+ {
+ if (!av.colSel.isVisible(r[0]))
+ {
+ // don't scroll - position isn't visible
+ return false;
+ }
+ }
+ }
+ if (!av.wrapAlignment)
+ {
+ if ((startv = av.getStartRes()) >= start)
+ {
+ setScrollValues(start - 1, seqIndex);
+ }
+ else if ((endv = av.getEndRes()) <= end)
+ {
+ setScrollValues(startv + 1 + end - endv, seqIndex);
+ }
+ else if ((starts = av.getStartSeq()) > seqIndex)
+ {
+ setScrollValues(av.getStartRes(), seqIndex);
+ }
+ else if ((ends = av.getEndSeq()) <= seqIndex)
+ {
+ setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
+ }
+ }
+ else
+ {
+ scrollToWrappedVisible(start);
+ }
+ }
+ if (redrawOverview && overviewPanel != null)
+ {
+ overviewPanel.setBoxPosition();
+ }
+ paintAlignment(redrawOverview);
+ return true;
+ }
+
+ void scrollToWrappedVisible(int res)
+ {
+ int cwidth = seqPanel.seqCanvas
+ .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+ if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth))
+ {
+ vscroll.setValue((res / cwidth));
+ av.startRes = vscroll.getValue() * cwidth;
+ }
+
+ }
+
+ /**
+ * 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.wrapAlignment)
+ {
+ annotationSpaceFillerHolder.setVisible(b);
+ annotationScroller.setVisible(b);
+ }
+ repaint();
+ }
+
+ /**
+ * automatically adjust annotation panel height for new annotation
+ * whilst ensuring the alignment is still visible.
+ */
+ 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();
+ paintAlignment(true);
+ }
+ /**
+ * calculate the annotation dimensions and refresh slider values accordingly.
+ * need to do repaints/notifys afterwards.
+ */
+ protected void validateAnnotationDimensions(boolean adjustPanelHeight) {
+ int height = annotationPanel.adjustPanelHeight();
+
+ if (hscroll.isVisible())
+ {
+ height += hscroll.getPreferredSize().height;
+ }
+ if (height > alignFrame.getHeight() / 2)
+ {
+ height = alignFrame.getHeight() / 2;
+ }
+ if (!adjustPanelHeight)
+ {
+ // maintain same window layout whilst updating sliders
+ height=annotationScroller.getSize().height;
+ }
+ hscroll.addNotify();
+
+ annotationScroller.setPreferredSize(new Dimension(annotationScroller
+ .getWidth(), height));
+
+ annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+ annotationSpaceFillerHolder.getWidth(), height));
+ annotationScroller.validate();// repaint();
+ annotationScroller.addNotify();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param wrap
+ * DOCUMENT ME!
+ */
+ public void setWrapAlignment(boolean wrap)
+ {
+ av.startSeq = 0;
+ scalePanelHolder.setVisible(!wrap);
+ hscroll.setVisible(!wrap);
+ idwidthAdjuster.setVisible(!wrap);
+
+ if (wrap)
+ {
+ annotationScroller.setVisible(false);
+ annotationSpaceFillerHolder.setVisible(false);
+ }
+ else if (av.showAnnotation)
+ {
+ annotationScroller.setVisible(true);
+ annotationSpaceFillerHolder.setVisible(true);
+ }
+
+ idSpaceFillerPanel1.setVisible(!wrap);
+
+ repaint();
+ }
+
+ // return value is true if the scroll is valid
+ public boolean scrollUp(boolean up)
+ {
+ if (up)
+ {
+ if (vscroll.getValue() < 1)
+ {
+ return false;
+ }
+
+ fastPaint = false;
+ vscroll.setValue(vscroll.getValue() - 1);
+ }
+ else
+ {
+ if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
+ {
+ return false;
+ }
+
+ fastPaint = false;
+ vscroll.setValue(vscroll.getValue() + 1);
+ }
+
+ fastPaint = true;
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param right
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean scrollRight(boolean right)
+ {
+ if (!right)
+ {
+ if (hscroll.getValue() < 1)
+ {
+ return false;
+ }
+
+ fastPaint = false;
+ hscroll.setValue(hscroll.getValue() - 1);
+ }
+ else
+ {
+ if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
+ {
+ return false;
+ }
+
+ fastPaint = false;
+ hscroll.setValue(hscroll.getValue() + 1);
+ }
+
+ fastPaint = true;
+
+ return true;
+ }
+
+ /**
+ * Adjust row/column scrollers to show a visible position in the alignment.
+ *
+ * @param x visible column to scroll to
+ * DOCUMENT ME!
+ * @param y visible row to scroll to
+ *
+ */
+ public void setScrollValues(int x, int y)
+ {
+ // System.err.println("Scroll to "+x+","+y);
+ if (av == null || av.alignment == null)
+ {
+ return;
+ }
+ int width = av.alignment.getWidth();
+ int height = av.alignment.getHeight();
+
+ if (av.hasHiddenColumns)
+ {
+ width = av.getColumnSelection().findColumnPosition(width);
+ }
+
+ av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) - 1);
+
+ hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
+ vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
+
+ 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;
+ }
+
+ hscroll.setValues(x, hextent, 0, width);
+ vscroll.setValues(y, vextent, 0, height);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void adjustmentValueChanged(AdjustmentEvent evt)
+ {
+
+ int oldX = av.getStartRes();
+ int oldY = av.getStartSeq();
+
+ if (evt.getSource() == hscroll)
+ {
+ int x = hscroll.getValue();
+ av.setStartRes(x);
+ av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
+ }
+
+ if (evt.getSource() == vscroll)
+ {
+ int offy = vscroll.getValue();
+
+ if (av.getWrapAlignment())
+ {
+ if (offy > -1)
+ {
+ int rowSize = seqPanel.seqCanvas
+ .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+ av.setStartRes(offy * rowSize);
+ av.setEndRes((offy + 1) * 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()
+ {
+ public void run()
+ {
+ setScrollValues(av.getStartRes(), av.getStartSeq());
+ }
+ });
+ }
+ }
+ else
+ {
+ av.setStartSeq(offy);
+ av.setEndSeq(offy
+ + (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
+ }
+ }
+
+ if (overviewPanel != null)
+ {
+ overviewPanel.setBoxPosition();
+ }
+
+ int scrollX = av.startRes - oldX;
+ int scrollY = av.startSeq - oldY;
+
+ if (av.getWrapAlignment() || !fastPaint)
+ {
+ repaint();
+ }
+ else
+ {
+ // Make sure we're not trying to draw a panel
+ // larger than the visible window
+ if (scrollX > av.endRes - av.startRes)
+ {
+ scrollX = av.endRes - av.startRes;
+ }
+ else if (scrollX < av.startRes - av.endRes)
+ {
+ scrollX = av.startRes - av.endRes;
+ }
+
+ if (scrollX != 0 || scrollY != 0)
+ {
+ idPanel.idCanvas.fastPaint(scrollY);
+ seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
+ scalePanel.repaint();
+
+ if (av.getShowAnnotation())
+ {
+ annotationPanel.fastPaint(scrollX);
+ }
+ }
+ }
+ }
+
+ public void paintAlignment(boolean updateOverview)
+ {
+ repaint();
+
+ if (updateOverview)
+ {
+ av.getStructureSelectionManager().sequenceColoursChanged(this);
+
+ if (overviewPanel != null)
+ {
+ overviewPanel.updateOverviewImage();
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ */
+ public void paintComponent(Graphics g)
+ {
+ invalidate();
+
+ Dimension d = idPanel.idCanvas.getPreferredSize();
+ idPanelHolder.setPreferredSize(d);
+ hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
+ validate();
+
+ if (av.getWrapAlignment())
+ {
+ int maxwidth = av.alignment.getWidth();
+
+ if (av.hasHiddenColumns)
+ {
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ }
+
+ int canvasWidth = seqPanel.seqCanvas
+ .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+ if (canvasWidth > 0)
+ {
+ int max = maxwidth
+ / seqPanel.seqCanvas
+ .getWrappedCanvasWidth(seqPanel.seqCanvas
+ .getWidth()) + 1;
+ vscroll.setMaximum(max);
+ vscroll.setUnitIncrement(1);
+ vscroll.setVisibleAmount(1);
+ }
+ }
+ else
+ {
+ setScrollValues(av.getStartRes(), av.getStartSeq());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pg
+ * DOCUMENT ME!
+ * @param pf
+ * DOCUMENT ME!
+ * @param pi
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws PrinterException
+ * DOCUMENT ME!
+ */
+ 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(pg, pwidth, pheight, pi);
+ }
+ else
+ {
+ return printUnwrapped(pg, pwidth, pheight, pi);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pg
+ * DOCUMENT ME!
+ * @param pwidth
+ * DOCUMENT ME!
+ * @param pheight
+ * DOCUMENT ME!
+ * @param pi
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws PrinterException
+ * DOCUMENT ME!
+ */
+ public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
+ throws PrinterException
+ {
+ int idWidth = getVisibleIdWidth();
+ FontMetrics fm = getFontMetrics(av.getFont());
+ int scaleHeight = av.charHeight + fm.getDescent();
+
+ pg.setColor(Color.white);
+ pg.fillRect(0, 0, pwidth, pheight);
+ pg.setFont(av.getFont());
+
+ // //////////////////////////////////
+ // / How many sequences and residues can we fit on a printable page?
+ int totalRes = (pwidth - idWidth) / av.getCharWidth();
+
+ int totalSeq = (int) ((pheight - scaleHeight) / av.getCharHeight()) - 1;
+
+ int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
+
+ // ///////////////////////////
+ // / Only print these sequences and residues on this page
+ int startRes;
+
+ // ///////////////////////////
+ // / Only print these sequences and residues on this page
+ int endRes;
+
+ // ///////////////////////////
+ // / Only print these sequences and residues on this page
+ int startSeq;
+
+ // ///////////////////////////
+ // / Only print these sequences and residues on this page
+ int endSeq;
+ startRes = (pi % pagesWide) * totalRes;
+ endRes = (startRes + totalRes) - 1;
+
+ if (endRes > (av.getAlignment().getWidth() - 1))
+ {
+ endRes = av.getAlignment().getWidth() - 1;
+ }
+
+ startSeq = (pi / pagesWide) * totalSeq;
+ endSeq = startSeq + totalSeq;
+
+ if (endSeq > av.getAlignment().getHeight())
+ {
+ endSeq = av.getAlignment().getHeight();
+ }
+
+ int pagesHigh = ((av.alignment.getHeight() / totalSeq) + 1) * pheight;
+
+ if (av.showAnnotation)
+ {
+ pagesHigh += annotationPanel.adjustPanelHeight() + 3;
+ }
+
+ pagesHigh /= pheight;
+
+ if (pi >= (pagesWide * pagesHigh))
+ {
+ return Printable.NO_SUCH_PAGE;
+ }
+
+ // draw Scale
+ pg.translate(idWidth, 0);
+ scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth,
+ scaleHeight);
+ pg.translate(-idWidth, scaleHeight);
+
+ // //////////////
+ // Draw the ids
+ Color currentColor = null;
+ Color currentTextColor = null;
+
+ pg.setFont(idPanel.idCanvas.idfont);
+
+ SequenceI seq;
+ for (int i = startSeq; i < endSeq; i++)
+ {
+ seq = av.getAlignment().getSequenceAt(i);
+ if ((av.getSelectionGroup() != null)
+ && av.getSelectionGroup().getSequences(null).contains(seq))
+ {
+ currentColor = Color.gray;
+ currentTextColor = Color.black;
+ }
+ else
+ {
+ currentColor = av.getSequenceColour(seq);
+ currentTextColor = Color.black;
+ }
+
+ pg.setColor(currentColor);
+ pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
+ av.getCharHeight());
+
+ pg.setColor(currentTextColor);
+
+ int xPos = 0;
+ if (av.rightAlignIds)
+ {
+ fm = pg.getFontMetrics();
+ xPos = idWidth
+ - fm.stringWidth(seq.getDisplayId(av.getShowJVSuffix()))
+ - 4;
+ }
+
+ pg.drawString(
+ seq.getDisplayId(av.getShowJVSuffix()),
+ xPos,
+ (((i - startSeq) * av.charHeight) + av.getCharHeight())
+ - (av.getCharHeight() / 5));
+ }
+
+ pg.setFont(av.getFont());
+
+ // draw main sequence panel
+ pg.translate(idWidth, 0);
+ seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
+
+ if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
+ {
+ pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
+ alabels.drawComponent((Graphics2D) pg, idWidth);
+ pg.translate(idWidth + 3, 0);
+ annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes + 1);
+ }
+
+ return Printable.PAGE_EXISTS;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pg
+ * DOCUMENT ME!
+ * @param pwidth
+ * DOCUMENT ME!
+ * @param pheight
+ * DOCUMENT ME!
+ * @param pi
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws PrinterException
+ * DOCUMENT ME!
+ */
+ public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
+ int pi) throws PrinterException
+ {
+
+ int annotationHeight = 0;
+ AnnotationLabels labels = null;
+ if (av.showAnnotation)
+ {
+ annotationHeight = annotationPanel.adjustPanelHeight();
+ labels = new AnnotationLabels(av);
+ }
+
+ int hgap = av.charHeight;
+ if (av.scaleAboveWrapped)
+ {
+ hgap += av.charHeight;
+ }
+
+ int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+ + annotationHeight;
+
+ int idWidth = getVisibleIdWidth();
+
+ int maxwidth = av.alignment.getWidth();
+ if (av.hasHiddenColumns)
+ {
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ }
+
+ int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth
+ - idWidth);
+
+ int totalHeight = cHeight * (maxwidth / resWidth + 1);
+
+ pg.setColor(Color.white);
+ pg.fillRect(0, 0, pwidth, pheight);
+ pg.setFont(av.getFont());
+
+ // //////////////
+ // Draw the ids
+ pg.setColor(Color.black);
+
+ pg.translate(0, -pi * pheight);
+
+ pg.setClip(0, pi * pheight, pwidth, pheight);
+
+ int ypos = hgap;
+
+ do
+ {
+ for (int i = 0; i < av.alignment.getHeight(); i++)
+ {
+ pg.setFont(idPanel.idCanvas.idfont);
+ SequenceI s = av.alignment.getSequenceAt(i);
+ String string = s.getDisplayId(av.getShowJVSuffix());
+ int xPos = 0;
+ if (av.rightAlignIds)
+ {
+ FontMetrics fm = pg.getFontMetrics();
+ xPos = idWidth - fm.stringWidth(string) - 4;
+ }
+ pg.drawString(string, xPos,
+ ((i * av.charHeight) + ypos + av.charHeight)
+ - (av.charHeight / 5));
+ }
+ if (labels != null)
+ {
+ pg.translate(-3, ypos
+ + (av.getAlignment().getHeight() * av.charHeight));
+
+ pg.setFont(av.getFont());
+ labels.drawComponent(pg, idWidth);
+ pg.translate(+3, -ypos
+ - (av.getAlignment().getHeight() * av.charHeight));
+ }
+
+ ypos += cHeight;
+ } while (ypos < totalHeight);
+
+ pg.translate(idWidth, 0);
+
+ seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight,
+ 0);
+
+ if ((pi * pheight) < totalHeight)
+ {
+ return Printable.PAGE_EXISTS;
+
+ }
+ else
+ {
+ return Printable.NO_SUCH_PAGE;
+ }
+ }
+
+ int getVisibleIdWidth()
+ {
+ return idPanel.getWidth() > 0 ? idPanel.getWidth()
+ : calculateIdWidth().width + 4;
+ }
+
+ void makeAlignmentImage(int type, File file)
+ {
+ int maxwidth = av.alignment.getWidth();
+ if (av.hasHiddenColumns)
+ {
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
+ }
+
+ int height = ((av.alignment.getHeight() + 1) * av.charHeight)
+ + scalePanel.getHeight();
+ int width = getVisibleIdWidth() + (maxwidth * av.charWidth);
+
+ if (av.getWrapAlignment())
+ {
+ height = getWrappedHeight();
+ if (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true"))
+ {
+ // TODO: JAL-244
+ width = alignFrame.getWidth() - vscroll.getPreferredSize().width
+ - alignFrame.getInsets().left
+ - alignFrame.getInsets().right;
+ }
+ else
+ {
+ width = seqPanel.getWidth() + getVisibleIdWidth();
+ }
+
+ }
+ else if (av.getShowAnnotation())
+ {
+ height += annotationPanel.adjustPanelHeight() + 3;
+ }
+
+ try
+ {
+
+ jalview.util.ImageMaker im;
+ if (type == jalview.util.ImageMaker.PNG)
+ {
+ im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
+ "Create PNG image from alignment", width, height, file,
+ null);
+ }
+ else
+ {
+ im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
+ "Create EPS file from alignment", width, height, file,
+ alignFrame.getTitle());
+ }
+
+ if (av.getWrapAlignment())
+ {
+ if (im.getGraphics() != null)
+ {
+ printWrappedAlignment(im.getGraphics(), width, height, 0);
+ im.writeImage();
+ }
+ }
+ else
+ {
+ if (im.getGraphics() != null)
+ {
+ printUnwrapped(im.getGraphics(), width, height, 0);
+ im.writeImage();
+ }
+ }
+ } catch (OutOfMemoryError err)
+ {
+ // Be noisy here.
+ System.out.println("########################\n" + "OUT OF MEMORY "
+ + file + "\n" + "########################");
+ new OOMWarning("Creating Image for " + file, err);
+ // System.out.println("Create IMAGE: " + err);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void makeEPS(File epsFile)
+ {
+ makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void makePNG(File pngFile)
+ {
+ makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
+ }
+
+ public void makePNGImageMap(File imgMapFile, String imageName)
+ {
+ // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
+ // ////////////////////////////////////////////
+ int idWidth = getVisibleIdWidth();
+ FontMetrics fm = getFontMetrics(av.getFont());
+ int scaleHeight = av.charHeight + fm.getDescent();
+
+ // Gen image map
+ // ////////////////////////////////
+ if (imgMapFile != null)
+ {
+ try
+ {
+ int s, sSize = av.alignment.getHeight(), res, alwidth = av.alignment
+ .getWidth(), g, gSize, f, fSize, sy;
+ StringBuffer text = new StringBuffer();
+ PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
+ out.println(jalview.io.HTMLOutput.getImageMapHTML());
+ out.println("<img src=\"" + imageName
+ + "\" border=\"0\" usemap=\"#Map\" >"
+ + "<map name=\"Map\">");
+
+ for (s = 0; s < sSize; s++)
+ {
+ sy = s * av.charHeight + scaleHeight;
+
+ SequenceI seq = av.alignment.getSequenceAt(s);
+ SequenceFeature[] features = seq.getDatasetSequence()
+ .getSequenceFeatures();
+ SequenceGroup[] groups = av.alignment.findAllGroups(seq);
+ for (res = 0; res < alwidth; res++)
+ {
+ text = new StringBuffer();
+ Object obj = null;
+ if (av.alignment.isNucleotide())
+ {
+ obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)
+ + "");
+ }
+ else
+ {
+ obj = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
+ + "");
+ }
+
+ if (obj == null)
+ {
+ continue;
+ }
+
+ String triplet = obj.toString();
+ int alIndex = seq.findPosition(res);
+ gSize = groups.length;
+ for (g = 0; g < gSize; g++)
+ {
+ if (text.length() < 1)
+ {
+ text.append("<area shape=\"rect\" coords=\""
+ + (idWidth + res * av.charWidth) + "," + sy + ","
+ + (idWidth + (res + 1) * av.charWidth) + ","
+ + (av.charHeight + sy) + "\""
+ + " onMouseOver=\"toolTip('" + alIndex + " "
+ + triplet);
+ }
+
+ if (groups[g].getStartRes() < res
+ && groups[g].getEndRes() > res)
+ {
+ text.append("<br><em>" + groups[g].getName() + "</em>");
+ }
+ }
+
+ if (features != null)
+ {
+ if (text.length() < 1)
+ {
+ text.append("<area shape=\"rect\" coords=\""
+ + (idWidth + res * av.charWidth) + "," + sy + ","
+ + (idWidth + (res + 1) * av.charWidth) + ","
+ + (av.charHeight + sy) + "\""
+ + " onMouseOver=\"toolTip('" + alIndex + " "
+ + triplet);
+ }
+ fSize = features.length;
+ for (f = 0; f < fSize; f++)
+ {
+
+ if ((features[f].getBegin() <= seq.findPosition(res))
+ && (features[f].getEnd() >= seq.findPosition(res)))
+ {
+ if (features[f].getType().equals("disulfide bond"))
+ {
+ if (features[f].getBegin() == seq.findPosition(res)
+ || features[f].getEnd() == seq
+ .findPosition(res))
+ {
+ text.append("<br>disulfide bond "
+ + features[f].getBegin() + ":"
+ + features[f].getEnd());
+ }
+ }
+ else
+ {
+ text.append("<br>");
+ text.append(features[f].getType());
+ if (features[f].getDescription() != null
+ && !features[f].getType().equals(
+ features[f].getDescription()))
+ {
+ text.append(" " + features[f].getDescription());
+ }
+
+ if (features[f].getValue("status") != null)
+ {
+ text.append(" (" + features[f].getValue("status")
+ + ")");
+ }
+ }
+ }
+
+ }
+ }
+ 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 = seqPanel.seqCanvas.getWidth();
+
+ if (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true"))
+ {
+ seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
+ - vscroll.getPreferredSize().width
+ - alignFrame.getInsets().left - alignFrame.getInsets().right;
+ }
+
+ int chunkWidth = seqPanel.seqCanvas
+ .getWrappedCanvasWidth(seqPanelWidth);
+
+ int hgap = av.charHeight;
+ if (av.scaleAboveWrapped)
+ {
+ hgap += av.charHeight;
+ }
+
+ int annotationHeight = 0;
+ if (av.showAnnotation)
+ {
+ annotationHeight = annotationPanel.adjustPanelHeight();
+ }
+
+ int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+ + annotationHeight;
+
+ int maxwidth = av.alignment.getWidth();
+ if (av.hasHiddenColumns)
+ {
+ maxwidth = av.getColumnSelection().findColumnPosition(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(seqPanel.seqCanvas);
+ PaintRefresher.RemoveComponent(idPanel.idCanvas);
+ PaintRefresher.RemoveComponent(this);
+ if (av != null)
+ {
+ jalview.structure.StructureSelectionManager ssm = av.getStructureSelectionManager();
+ ssm.removeStructureViewerListener(seqPanel, null);
+ ssm.removeSelectionListener(seqPanel);
+ av.alignment = null;
+ av = null;
+ }
+ else
+ {
+ if (Cache.log.isDebugEnabled())
+ {
+ Cache.log.warn("Closing alignment panel which is already closed.");
+ }
+ }
+ }
+
+ /**
+ * hides or shows dynamic annotation rows based on groups and av state flags
+ */
+ public void updateAnnotation()
+ {
+ updateAnnotation(false);
+ }
+
+ public void updateAnnotation(boolean applyGlobalSettings)
+ {
+ // TODO: this should be merged with other annotation update stuff - that
+ // sits on AlignViewport
+ boolean updateCalcs = false;
+ boolean conv = av.isShowGroupConservation();
+ boolean cons = av.isShowGroupConsensus();
+ boolean showprf = av.isShowSequenceLogo();
+ boolean showConsHist = av.isShowConsensusHistogram();
+
+ boolean sortg = true;
+
+ // remove old automatic annotation
+ // add any new annotation
+
+ Vector gr = av.alignment.getGroups(); // OrderedBy(av.alignment.getSequencesArray());
+ // intersect alignment annotation with alignment groups
+
+ AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation();
+ Hashtable oldrfs = new Hashtable();
+ if (aan != null)
+ {
+ for (int an = 0; an < aan.length; an++)
+ {
+ if (aan[an].autoCalculated && aan[an].groupRef != null)
+ {
+ oldrfs.put(aan[an].groupRef, aan[an].groupRef);
+ av.alignment.deleteAnnotation(aan[an]);
+ aan[an] = null;
+ }
+ }
+ }
+ SequenceGroup sg;
+ if (gr != null)
+ {
+ for (int g = 0; g < gr.size(); g++)
+ {
+ updateCalcs = false;
+ sg = (SequenceGroup) gr.elementAt(g);
+ if (applyGlobalSettings || !oldrfs.containsKey(sg))
+ {
+ // set defaults for this group's conservation/consensus
+ sg.setshowSequenceLogo(showprf);
+ sg.setShowConsensusHistogram(showConsHist);
+ }
+ if (conv)
+ {
+ updateCalcs = true;
+ av.alignment.addAnnotation(sg.getConservationRow(), 0);
+ }
+ if (cons)
+ {
+ updateCalcs = true;
+ av.alignment.addAnnotation(sg.getConsensus(), 0);
+ }
+ // refresh the annotation rows
+ if (updateCalcs)
+ {
+ sg.recalcConservation();
+ }
+ }
+ }
+ oldrfs.clear();
+ adjustAnnotationHeight();
+ }
+
+ @Override
+ public AlignmentI getAlignment()
+ {
+ return av.alignment;
+ }
+
+ /**
+ * get the name for this view
+ * @return
+ */
+ public String getViewName()
+ {
+ return av.viewName;
+ }
+
+ /**
+ * Make/Unmake this alignment panel the current input focus
+ * @param b
+ */
+ public void setSelected(boolean b)
+ {
+ try {
+ alignFrame.setSelected(b);
+ } catch (Exception ex) {};
+
+ if (b)
+ {
+ alignFrame.setDisplayedView(this);
+ }
+ }
+
+ @Override
+ public StructureSelectionManager getStructureSelectionManager()
+ {
+ return av.getStructureSelectionManager();
+ }
+}
git://source.jalview.org / jalview.git / blobdiff