X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=f7c465cdc4cfc6e785c893b2983b4fe18a14dcb8;hp=af24c9ff5c60b9b66c5a906a911109a874c172fb;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hpb=df7880a58e6b16d65f9ed8dbe4433efffbe8abec diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java old mode 100755 new mode 100644 index af24c9f..f7c465c --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,1107 +1,1453 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ -package jalview.gui; - -import jalview.datamodel.*; - -import jalview.jbgui.*; - -import jalview.schemes.*; - -import java.awt.*; -import java.awt.event.*; -import java.awt.print.*; - -import java.io.*; - -import javax.swing.*; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class AlignmentPanel extends GAlignmentPanel - implements AdjustmentListener, Printable -{ - 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); - - annotationSpaceFillerHolder.setPreferredSize(annotationPanel. - getPreferredSize()); - annotationScroller.setPreferredSize(annotationPanel.getPreferredSize()); - annotationScroller.setViewportView(annotationPanel); - annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER); - - fontChanged(); - - scalePanelHolder.add(scalePanel, BorderLayout.CENTER); - seqPanelHolder.add(seqPanel, BorderLayout.CENTER); - - setScrollValues(0, 0); - - annotationPanel.adjustPanelHeight(); - annotationSpaceFillerHolder.setPreferredSize(annotationPanel. - getPreferredSize()); - annotationScroller.setPreferredSize(annotationPanel. - getPreferredSize()); - setAnnotationVisible(av.getShowAnnotation()); - - hscroll.addAdjustmentListener(this); - vscroll.addAdjustmentListener(this); - - af.addKeyListener(new KeyAdapter() - { - public void keyPressed(KeyEvent evt) - { - switch (evt.getKeyCode()) - { - case 27: // escape key - av.setSelectionGroup(null); - repaint(); - - break; - - case KeyEvent.VK_DOWN: - alignFrame.moveSelectedSequences(false); - - break; - - case KeyEvent.VK_UP: - alignFrame.moveSelectedSequences(true); - - break; - - case KeyEvent.VK_BACK_SPACE: - case KeyEvent.VK_DELETE: - alignFrame.cut_actionPerformed(null); - break; - - case KeyEvent.VK_P: - seqPanel.seqCanvas.increaseAARatio(); - break; - case KeyEvent.VK_L: - seqPanel.seqCanvas.decreaseAARation(); - break; - } - } - }); - } - - /** - * 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 (av.getWrapAlignment()) - { - int max = av.alignment.getWidth() / - seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()); - vscroll.setMaximum(max); - vscroll.setUnitIncrement(1); - vscroll.setVisibleAmount(1); - } - else - { - setScrollValues(av.getStartRes(), av.getStartSeq()); - } - - if (overviewPanel != null) - overviewPanel.setBoxPosition(); - - repaint(); - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Dimension calculateIdWidth() - { - Container c = new Container(); - - FontMetrics fm = c.getFontMetrics(av.font); - 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(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(idWidth, 12); - } - - /** - * DOCUMENT ME! - * - * @param results DOCUMENT ME! - */ - public void highlightSearchResults(int[] results) - { - seqPanel.seqCanvas.highlightSearchResults(results); - - // do we need to scroll the panel? - if (results != null) - { - SequenceI seq = av.alignment.getSequenceAt(results[0]); - int start = seq.findIndex(results[1]) - 1; - int end = seq.findIndex(results[2]) - 1; - - if ( (av.getStartRes() > start) || (av.getEndRes() < end) || - ( (av.getStartSeq() > results[0]) || - (av.getEndSeq() < results[0]))) - { - setScrollValues(start, results[0]); - } - } - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public OverviewPanel getOverviewPanel() - { - return overviewPanel; - } - - /** - * DOCUMENT ME! - * - * @param op DOCUMENT ME! - */ - public void setOverviewPanel(OverviewPanel op) - { - overviewPanel = op; - } - - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setAnnotationVisible(boolean b) - { - if (!av.wrapAlignment) - { - annotationSpaceFillerHolder.setVisible(b); - annotationScroller.setVisible(b); - } - repaint(); - } - - /** - * 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; - } - - /** - * DOCUMENT ME! - * - * @param x DOCUMENT ME! - * @param y DOCUMENT ME! - */ - public void setScrollValues(int x, int y) - { - av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - - 1); - - hextent = seqPanel.seqCanvas.getWidth() / av.charWidth; - vextent = seqPanel.seqCanvas.getHeight() / av.charHeight; - - if (hextent > av.alignment.getWidth()) - { - hextent = av.alignment.getWidth(); - } - - if (vextent > av.alignment.getHeight()) - { - vextent = av.alignment.getHeight(); - } - - if ( (hextent + x) > av.getAlignment().getWidth()) - { - x = av.getAlignment().getWidth() - hextent; - } - - if ( (vextent + y) > av.getAlignment().getHeight()) - { - y = av.getAlignment().getHeight() - vextent; - } - - if (y < 0) - { - y = 0; - } - - if (x < 0) - { - x = 0; - } - - hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth()); - vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight()); - } - - /** - * 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()) - { - int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel. - seqCanvas.getWidth()); - av.setStartRes(vscroll.getValue() * rowSize); - av.setEndRes( (vscroll.getValue() + 1) * rowSize); - } - else - { - av.setStartSeq(offy); - av.setEndSeq(offy + - (seqPanel.seqCanvas.getHeight() / av.getCharHeight())); - } - } - - if (overviewPanel != null) - { - overviewPanel.setBoxPosition(); - } - - int xShift = av.getStartRes() - oldX; - int yShift = av.getStartSeq() - oldY; - - if ( (xShift != 0 && yShift != 0) || - (Math.abs(xShift) > av.getEndRes() - av.getStartRes() - || Math.abs(yShift) > av.getEndSeq() - av.getStartSeq()) - || av.getWrapAlignment() - || !fastPaint) - { - // Either no shift at all, or shift greater than visible amount - repaint(); - } - else - { - idPanel.idCanvas.fastPaint(yShift); - seqPanel.seqCanvas.fastPaint(xShift, yShift); - - scalePanel.repaint(); - - if (av.getShowAnnotation()) - { - annotationPanel.fastPaint(xShift); - } - } - } - - /** - * 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 max = av.alignment.getWidth() / - seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) +1; - vscroll.setMaximum(max); - vscroll.setUnitIncrement(1); - vscroll.setVisibleAmount(1); - } - else - { - setScrollValues(av.getStartRes(), av.getStartSeq()); - } - - - if( this.getVisibleRect().getBounds() == g.getClipBounds() ) - { - if (overviewPanel != null) - overviewPanel.updateOverviewImage(); - } - } - - /** - * 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 = calculateIdWidth().width + 4; - 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; - - for (int i = startSeq; i < endSeq; i++) - { - if ( (av.getSelectionGroup() != null) && - av.getSelectionGroup().sequences.contains( - av.getAlignment().getSequenceAt(i))) - { - currentColor = Color.gray; - currentTextColor = Color.black; - } - else - { - currentColor = av.getAlignment().getSequenceAt(i).getColor(); - currentTextColor = Color.black; - } - - pg.setColor(currentColor); - pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth, - av.getCharHeight()); - - pg.setColor(currentTextColor); - - String string = av.getAlignment().getSequenceAt(i).getDisplayId - ( av.getShowJVSuffix()); - - pg.drawString(string, 0, - ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) - - (av.getCharHeight() / 5)); - } - - // draw main sequence panel - pg.translate(idWidth, 0); - seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, - startRes, startSeq, 0); - - if (av.showAnnotation && (endSeq == av.alignment.getHeight())) - { - pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight + 3); - alabels.drawComponent( (Graphics2D) pg, idWidth); - pg.translate(idWidth, 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 = calculateIdWidth().width + 4; - - int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth - - idWidth); - - int totalHeight = cHeight * (av.alignment.getWidth() / 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; - Font italic = new Font(av.getFont().getName(), Font.ITALIC, - av.getFont().getSize()); - pg.setFont(italic); - - do - { - for (int i = 0; i < av.alignment.getHeight(); i++) - { - SequenceI s = av.alignment.getSequenceAt(i); - String string = s.getDisplayId( av.getShowJVSuffix()); - - pg.drawString(string, 0, - ( (i * av.charHeight) + ypos + av.charHeight) - - (av.charHeight / 5)); - } - if (labels != null) - { - pg.translate(0, - ypos + - (av.getAlignment().getHeight() * av.charHeight)); - - pg.setFont(av.getFont()); - labels.drawComponent(pg, idWidth); - pg.setFont(italic); - pg.translate(0, - -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; - } - } - - void makeAlignmentImage(int type, File file) - { - int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30; - int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth); - - if (idPanel.getWidth() == 0) - { - width += calculateIdWidth().getWidth() + 4; - } - - if (av.getWrapAlignment()) - { - height = getWrappedHeight(); - width = seqPanel.getWidth() + idPanel.getWidth(); - } - else if (av.getShowAnnotation()) - { - height += annotationPanel.adjustPanelHeight() + 3; - } - - 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() ); - - try - { - if (av.getWrapAlignment()) - { - if(im.getGraphics()!=null) - printWrappedAlignment(im.getGraphics(), width, height, 0); - } - else - { - if(im.getGraphics()!=null) - printUnwrapped(im.getGraphics(), width, height, 0); - } - - im.writeImage(); - } - catch (OutOfMemoryError err) - { - System.out.println("########################\n" - + "OUT OF MEMORY " + file + "\n" - + "########################"); - - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Out of Memory Creating Image!!" - + - "\nSee help files for increasing Java Virtual Machine memory." - , "Out of memory", - JOptionPane.WARNING_MESSAGE); - System.out.println("Create IMAGE: " + err); - System.gc(); - - } - 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 = calculateIdWidth().width + 4; - 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("" - + ""); - - for (s = 0; s < sSize; s++) - { - sy = s * av.charHeight + scaleHeight; - - SequenceI seq = av.alignment.getSequenceAt(s); - java.util.Vector features = seq.getDatasetSequence().getSequenceFeatures(); - SequenceGroup[] groups = av.alignment.findAllGroups(seq); - for(res =0; resres) - text.append("
" + groups[g].getName() + ""); - } - - if (features != null) - { - if(text.length()<1) - { - text.append("= seq.findPosition(res))) - { - if (sf.getType().equals("disulfide bond")) - { - if (sf.getBegin() == seq.findPosition(res) - || sf.getEnd() == seq.findPosition(res)) - { - text.append("
disulfide bond " + sf.getBegin() + ":" + - sf.getEnd()); - } - } - else - { - text.append("
"); - text.append(sf.getType()); - if (sf.getDescription() != null && !sf.getType().equals(sf.getDescription())) - text.append(" " + sf.getDescription()); - - if (sf.getStatus() != null && sf.getStatus().length()>0) - { - text.append(" (" + sf.getStatus() + ")"); - } - } - } - - } - } - if(text.length()>1) - { - text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">"); - out.println(text.toString()); - } - } - } - out.println(""); - out.close(); - - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } ///////////END OF IMAGE MAP - - } - - int getWrappedHeight() - { - - int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth( - seqPanel.seqCanvas.getWidth()); - - 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 height = ( (av.alignment.getWidth() / chunkWidth) + 1) * cHeight; - - return height; - } - - /** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ - class Preview - extends JFrame - { - /** - * Creates a new Preview object. - * - * @param image DOCUMENT ME! - */ - public Preview(Image image) - { - setResizable(true); - setSize(image.getWidth(this), image.getHeight(this)); - setVisible(true); - getContentPane().setLayout(new BorderLayout()); - getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER); - validate(); - repaint(); - } - } - - /** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ - class PreviewPanel - extends JPanel - { - Image image; - - /** - * Creates a new PreviewPanel object. - * - * @param image DOCUMENT ME! - */ - public PreviewPanel(Image image) - { - this.image = image; - } - - /** - * DOCUMENT ME! - * - * @param g DOCUMENT ME! - */ - public void paintComponent(Graphics g) - { - if (image != null) - { - g.drawImage(image, 0, 0, this); - } - else - { - System.out.println("DEBUG:image is null"); - } - } - } -} +/* + * 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 . + */ +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("" + + ""); + + 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(" res) + { + text.append("
" + groups[g].getName() + ""); + } + } + + if (features != null) + { + if (text.length() < 1) + { + text.append("= 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("
disulfide bond " + + features[f].getBegin() + ":" + + features[f].getEnd()); + } + } + else + { + text.append("
"); + 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(""); + 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(); + } +}