X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=fae6dfc9fcd149b2d14ac019c5abb6eb31591050;hb=7e129811d6ff01074428462284dffc2a6c2395a4;hp=fcb5a57a4849009c96b240c5f8ce0ffc9b584276;hpb=bfdb9a55949b38a89878959278a8b8ed82a55e49;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index fcb5a57..fae6dfc 100755 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,416 +1,1057 @@ +/* + * 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.jbgui.GAlignmentPanel; -import jalview.schemes.*; -import jalview.analysis.*; import jalview.datamodel.*; + +import jalview.jbgui.*; + +import jalview.schemes.*; + +import org.jibble.epsgraphics.*; + import java.awt.*; import java.awt.event.*; +import java.awt.image.*; import java.awt.print.*; -public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable +import java.io.*; + +import javax.imageio.*; + +import javax.swing.*; + + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class AlignmentPanel extends GAlignmentPanel + implements AdjustmentListener, Printable { + 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); - AlignViewport av; - OverviewPanel overviewPanel; - SeqPanel seqPanel; - IdPanel idPanel; - public AlignFrame alignFrame; - ScalePanel scalePanel; - ScorePanel scorePanel; - - public AlignmentPanel(AlignFrame af, AlignViewport av) - { - alignFrame = af; - this.av = av; - seqPanel = new SeqPanel (av, this); - idPanel = new IdPanel (av, this); - scalePanel = new ScalePanel(av, this); - scorePanel = new ScorePanel(av); - - idPanelHolder.add(idPanel, BorderLayout.CENTER); - idPanel.addNotify(); - scalePanelHolder.add(scalePanel, BorderLayout.CENTER); - scorePanelHolder.add(scorePanel, BorderLayout.CENTER); - seqPanelHolder.add(seqPanel, BorderLayout.CENTER); - setScrollValues(0,0); - - hscroll.addAdjustmentListener(this); - vscroll.addAdjustmentListener(this); - - addComponentListener(new ComponentAdapter() - { - public void componentResized(ComponentEvent evt) - { - RefreshPanels(); - } - }); - } - - public void highlightSearchResults(int [] results) - { - seqPanel.seqCanvas.highlightSearchResults( results ); - - // do we need to scroll the panel? - if(results!=null && (av.getStartSeq()>results[0] - || av.getEndSeq()results[1] - || av.getEndRes() 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); } - else + + /** + * DOCUMENT ME! + * + * @param results DOCUMENT ME! + */ + public void highlightSearchResults(int[] results) { - SequenceGroup sg = av.alignment.findGroup((Sequence)av.sel.sequenceAt(0)); + seqPanel.seqCanvas.highlightSearchResults(results); - if( isNewSelection(sg) ) - { - sg = av.getAlignment().addGroup(); - for (int i=0; i < av.getSelection().size(); i++) + // do we need to scroll the panel? + if (results != null) { - av.alignment.removeFromGroup(av.alignment.findGroup( (Sequence) av. - sel.sequenceAt(i)), - (Sequence) av.sel.sequenceAt(i)); - av.alignment.addToGroup(sg, (Sequence) av.sel.sequenceAt(i)); + 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; + } - sg.cs = cs; + /** + * DOCUMENT ME! + * + * @param op DOCUMENT ME! + */ + public void setOverviewPanel(OverviewPanel op) + { + overviewPanel = op; + } - // Selection is made, we only want to change the conservationColour for selected group - if( showConservation - && !(sg.cs instanceof ConservationColourScheme) - && !(sg.cs instanceof Blosum62ColourScheme)) - { - Conservation c = sg.getConservation(); - Alignment al = (Alignment) av.getAlignment(); - - c = new Conservation("All", al.cons, - ResidueProperties.propHash, 3, sg.sequences, 0, - al.getWidth() ); - c.calculate(); - c.verdict(false, 100); - sg.setConservation(c); - sg.cs = new ConservationColourScheme(sg); + /** + * DOCUMENT ME! + * + * @param b DOCUMENT ME! + */ + public void setAnnotationVisible(boolean b) + { + annotationSpaceFillerHolder.setVisible(b); + annotationScroller.setVisible(b); } - else if( !showConservation && sg.cs instanceof ConservationColourScheme) + + /** + * DOCUMENT ME! + * + * @param wrap DOCUMENT ME! + */ + public void setWrapAlignment(boolean wrap) { - ConservationColourScheme ccs = (ConservationColourScheme)sg.cs; - sg.cs = ccs.cs; + 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(); } - } - repaint(); - } - boolean isNewSelection(SequenceGroup sg) - { - if(sg==null) - return true; - if(sg.getSize()!=av.getSelection().size()) - return true; + // return value is true if the scroll is valid + public boolean scrollUp(boolean up) + { + if (up) + { + if (vscroll.getValue() < 1) + { + return false; + } - for(int i=0; i= av.getAlignment().getHeight()) + { + return false; + } - return false; - } + fastPaint = false; + vscroll.setValue(vscroll.getValue() + 1); + } + fastPaint = true; - public ColourSchemeI getColourScheme() - { - if(av.getSelection().size()>0) - return av.alignment.findGroup((Sequence)av.sel.sequenceAt(0)).cs; - else - return seqCanvas.globalColorScheme; - } -*/ + return true; + } -/* public void setColourScheme(jalview.schemes.ColourSchemeI cs, boolean conservation) - { - seqPanel.setColourScheme(cs, conservation); + /** + * DOCUMENT ME! + * + * @param right DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean scrollRight(boolean right) + { + if (right) + { + if (hscroll.getValue() < 1) + { + return false; + } - av.setGlobalColourScheme(cs); + fastPaint = false; + hscroll.setValue(hscroll.getValue() - 1); + } + else + { + if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth()) + { + return false; + } + + fastPaint = false; + hscroll.setValue(hscroll.getValue() + 1); + } - if(overviewPanel!=null) - overviewPanel.updateOverviewImage(); - } + fastPaint = true; - void updateResidueView() - { - if (viewport.getSelection().size() == 0) - { - for (int i = 0; i < viewport.alignment.getGroups().size(); i++) + 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()) { - SequenceGroup sg = (SequenceGroup) viewport.alignment.getGroups().elementAt(i); - sg.setDisplayBoxes( viewBoxesMenuItem.isSelected() ); - sg.setDisplayText( viewTextMenuItem.isSelected() ); - sg.setColourText( colourTextMenuItem.isSelected() ); + hextent = av.alignment.getWidth(); } - } - else - { - SequenceGroup sg = viewport.alignment.findGroup( (Sequence) viewport.sel.sequenceAt(0)); - if (alignPanel.seqPanel.isNewSelection(sg)) + + if (vextent > av.alignment.getHeight()) { - sg = viewport.getAlignment().addGroup(); - for (int i = 0; i < viewport.getSelection().size(); i++) - { - viewport.alignment.removeFromGroup(viewport.alignment.findGroup( ( - Sequence) viewport.sel.sequenceAt(i)), - (Sequence) viewport.sel.sequenceAt( - i)); - viewport.alignment.addToGroup(sg, - (Sequence) viewport.sel.sequenceAt(i)); - } + vextent = av.alignment.getHeight(); } - sg.setDisplayBoxes(viewBoxesMenuItem.isSelected()); - sg.setDisplayText(viewTextMenuItem.isSelected()); - sg.setColourText(colourTextMenuItem.isSelected()); - } - alignPanel.RefreshPanels(); - }*/ + 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; + } - public void RefreshPanels() - { - invalidate(); - seqPanel.seqCanvas.paintFlag = true; - idPanel.idCanvas.paintFlag = true; - idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() ); - setScrollValues(av.getStartRes(), av.getStartSeq()); - av.getConsensus(true); - validate(); - repaint(); - if(overviewPanel!=null) - overviewPanel.updateOverviewImage(); + if (x < 0) + { + x = 0; + } - } + hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth()); + vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight()); + } - int hextent = 0; - int vextent = 0; - public void setScrollValues(int x, int y) - { - hextent = seqPanel.seqCanvas.getWidth()/av.getCharWidth(); - vextent = seqPanel.seqCanvas.getHeight()/av.getCharHeight(); + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void adjustmentValueChanged(AdjustmentEvent evt) + { - if(hextent+x > av.getAlignment().getWidth()) - x = av.getAlignment().getWidth()- hextent; + int oldX = av.getStartRes(); + int oldY = av.getStartSeq(); - if(vextent+y > av.getAlignment().getHeight()) - y = av.getAlignment().getHeight() - vextent; + if (evt.getSource() == hscroll) + { + int x = hscroll.getValue(); + av.setStartRes(x); + av.setEndRes((x + + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1); + } - if(y<0) - y = 0; + 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(x<0) - x=0; + if (overviewPanel != null) + { + overviewPanel.setBoxPosition(); + } - hscroll.setValues(x,hextent,0,av.getAlignment().getWidth()); - vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() ); - repaint(); + 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(); - public void adjustmentValueChanged(AdjustmentEvent evt) - { + if (av.getShowAnnotation()) + { + annotationPanel.fastPaint(xShift); + } + } + } - if (evt.getSource() == hscroll) + /** + * DOCUMENT ME! + * + * @param g DOCUMENT ME! + */ + public void paintComponent(Graphics g) { - int x = hscroll.getValue(); - av.setStartRes(x); - av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1); + 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()); + vscroll.setMaximum(max); + vscroll.setUnitIncrement(1); + vscroll.setVisibleAmount(1); + } + else + { + setScrollValues(av.getStartRes(), av.getStartSeq()); + } } - if (evt.getSource() == vscroll) + /** + * 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 { - int offy = vscroll.getValue(); - av.setStartSeq(offy); - av.setEndSeq(offy + seqPanel.seqCanvas.getHeight()/av.getCharHeight()); + 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(); - if(overviewPanel!=null) - overviewPanel.setBoxPosition(); + pg.setColor(Color.white); + pg.fillRect(0, 0, pwidth, pheight); + pg.setFont(av.getFont()); - seqPanel.seqCanvas.paintFlag=true; - repaint(); - } + //////////////////////////////////// + /// 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; - public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException - { + int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1; - pg.translate((int)pf.getImageableX(), (int)pf.getImageableY()); + ///////////////////////////// + /// Only print these sequences and residues on this page + int startRes; - int pwidth = (int)pf.getImageableWidth(); - int pheight = (int)pf.getImageableHeight(); - int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth(); + ///////////////////////////// + /// Only print these sequences and residues on this page + int endRes; - pg.setColor(Color.white); - pg.fillRect(0,0,pwidth, pheight); - pg.setFont( av.getFont() ); + ///////////////////////////// + /// Only print these sequences and residues on this page + int startSeq; - //////////////////////////////////// - /// How many sequences and residues can we fit on a printable page? - int totalRes = (pwidth - idWidth)/av.getCharWidth(); - int totalSeq = (int)((pheight - 30)/av.getCharHeight())-1; - int pagesWide = av.getAlignment().getWidth() / totalRes +1; - int pagesHigh = av.getAlignment().getHeight() / totalSeq +1; + ///////////////////////////// + /// Only print these sequences and residues on this page + int endSeq; + startRes = (pi % pagesWide) * totalRes; + endRes = (startRes + totalRes) - 1; - if (pi >= pagesWide*pagesHigh) - return Printable.NO_SUCH_PAGE; + if (endRes > (av.getAlignment().getWidth() - 1)) + { + endRes = av.getAlignment().getWidth() - 1; + } - ///////////////////////////// - /// Only print these sequences and residues on this page - int startRes, endRes, startSeq, endSeq; - startRes = (pi % pagesWide) * totalRes; - endRes = startRes + totalRes-1; - if(endRes>av.getAlignment().getWidth()) - endRes = av.getAlignment().getWidth(); + startSeq = (pi / pagesWide) * totalSeq; + endSeq = startSeq + totalSeq; - startSeq = (pi / pagesWide) * totalSeq; - endSeq = startSeq + totalSeq; - if(endSeq > av.getAlignment().getHeight()) - endSeq = av.getAlignment().getHeight(); + if (endSeq > av.getAlignment().getHeight()) + { + endSeq = av.getAlignment().getHeight(); + } + int pagesHigh = ((av.alignment.getHeight() / totalSeq) + 1) * pheight; - //////////////// - //draw Scale - pg.translate(idWidth,0); - scalePanel.scaleCanvas.drawScale(pg, startRes, endRes, pwidth-idWidth); + if (av.showAnnotation) + { + pagesHigh += annotationPanel.getHeight(); + } + + pagesHigh /= pheight; - pg.translate(-idWidth, 30); - //////////////// - // Draw the ids - Color currentColor=null; - Color currentTextColor=null; - for(int i=startSeq; i= (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).getName(); + + if (av.getShowFullId()) + { + string = av.getAlignment().getSequenceAt(i).getDisplayId(); + } + + 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); + alabels.drawComponent((Graphics2D) pg); + 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 { - if (av.getSelection().contains(av.getAlignment().getSequenceAt(i))) + int idWidth = calculateIdWidth().width + 4; + + int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth - + idWidth); + int totalHeight = totalHeight = (av.alignment.getHeight() + 2) * ((av.alignment.getWidth() / resWidth) + + 1) * av.charHeight; + + 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 = 2 * av.charHeight; + + do + { + for (int i = 0; i < av.alignment.getHeight(); i++) + { + SequenceI s = av.alignment.getSequenceAt(i); + String string = s.getName(); + + if (av.getShowFullId()) + { + string = s.getDisplayId(); + } + + pg.drawString(string, 0, + ((i * av.charHeight) + ypos + av.charHeight) - + (av.charHeight / 5)); + } + + ypos += ((av.alignment.getHeight() + 2) * av.charHeight); + } + 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; + } + } + + /** + * DOCUMENT ME! + */ + public void makeEPS(File epsFile) + { + if(epsFile == null) + { + jalview.io.JalviewFileChooser chooser = new jalview.io. + JalviewFileChooser(jalview.bin.Cache.getProperty( + "LAST_DIRECTORY"), new String[] + {"eps"}, + new String[] + {"Encapsulated Postscript"}, + "Encapsulated Postscript"); + chooser.setFileView(new jalview.io.JalviewFileView()); + chooser.setDialogTitle("Create EPS file from alignment"); + chooser.setToolTipText("Save"); + + int value = chooser.showSaveDialog(this); + + if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION) + { + return; + } + + epsFile = chooser.getSelectedFile(); + + jalview.bin.Cache.setProperty("LAST_DIRECTORY", + chooser.getSelectedFile().getParent()); + } + + int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30; + int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth); + + if (av.getWrapAlignment()) + { + height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) * + av.chunkHeight; + width = seqPanel.getWidth() + idPanel.getWidth(); + + } + + + if (av.getShowAnnotation()) + { + height += annotationPanel.getPreferredSize().height; + } + + try + { + FileOutputStream out = new FileOutputStream(epsFile); + EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width, + height); + + if (av.getWrapAlignment()) + { + printWrappedAlignment(pg, width, height, 0); + } + else + { + printUnwrapped(pg, width, height, 0); + } + + pg.flush(); + pg.close(); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + + + 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 + { + PrintWriter out = new PrintWriter(new FileWriter(imgMapFile)); + out.println(jalview.io.HTMLOutput.getImageMapHTML()); + out.println("" + +""); + + for (int s = 0; s < av.alignment.getHeight(); s++) + { + SequenceI seq = av.alignment.getSequenceAt(s); + SequenceGroup[] groups = av.alignment.findAllGroups(seq); + for (int i = 0; i < groups.length; i++) + { + int sy = s * av.charHeight + scaleHeight; + for (int res = groups[i].getStartRes(); + res < groups[i].getEndRes() + 1; res++) + { + int alIndex = seq.findPosition(res); + Object obj = ResidueProperties.aa2Triplet.get( + seq.getCharAt(res) + ""); + if (obj == null) + continue; + + String triplet = obj.toString(); + + out.println( + "" + groups[i].getName() + + "')\"; onMouseOut=\"toolTip()\"; " + + " href=\"#\">"); + } + } + } + + out.println(""); + out.close(); + + } + catch (Exception ex) + { + ex.printStackTrace(); + } + }///////////END OF IMAGE MAP + + } + + /** + * DOCUMENT ME! + */ + public void makePNG(File pngFile) + { + if(pngFile==null) { - currentColor = Color.gray; - currentTextColor = Color.black; + jalview.io.JalviewFileChooser chooser = new jalview.io. + JalviewFileChooser(jalview.bin.Cache.getProperty( + "LAST_DIRECTORY"), new String[] + {"png"}, + new String[] + {"Portable network graphics"}, + "Portable network graphics"); + chooser.setFileView(new jalview.io.JalviewFileView()); + chooser.setDialogTitle("Create EPS file from alignment"); + chooser.setToolTipText("Save"); + + int value = chooser.showSaveDialog(this); + + if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION) + { + return; + } + + pngFile = chooser.getSelectedFile(); + + jalview.bin.Cache.setProperty("LAST_DIRECTORY", + chooser.getSelectedFile().getParent()); } - else + + + + int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30; + int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth); + + if (av.getWrapAlignment()) { - currentColor = av.getAlignment().getSequenceAt(i).getColor(); - currentTextColor = Color.black; + height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) * + av.chunkHeight; + width = seqPanel.getWidth() + idPanel.getWidth(); + } - pg.setColor(currentColor); - pg.fillRect(0, jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()), - idWidth, - av.getCharHeight()); - pg.setColor(currentTextColor); + if (av.getShowAnnotation()) + { + height += annotationPanel.getPreferredSize().height; + } - String string = av.getAlignment().getSequenceAt(i).getDisplayId(); - pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight - (startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5)); - } + try + { + + FileOutputStream out = new FileOutputStream(pngFile); + + BufferedImage bi = new BufferedImage(width, height, + BufferedImage.TYPE_INT_RGB); + Graphics2D png = (Graphics2D) bi.getGraphics(); + + png.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); - // draw main sequence panel - pg.translate(idWidth,0); - pg.setClip(0,0,pwidth-idWidth, pheight); - seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0); + if (av.getWrapAlignment()) + { + printWrappedAlignment(png, width, height, 0); + } + else + { + printUnwrapped(png, width, height, 0); + } + + ImageIO.write(bi, "png", out); + out.close(); + } + catch(OutOfMemoryError err) + { + System.out.println("########################\n" + +"OUT OF MEMORY "+pngFile+"\n" + +"########################"); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } +} - return Printable.PAGE_EXISTS; - } +/** + * 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"); + } + } +}