X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=eaa685dc86ea638ddaa52f55182da1228d39642b;hb=12e7f97678ce85b0238f987d5f4eaf18512a0b94;hp=0cbdfbe3e3fe813a9b4433e4496b14d4e8c3ead8;hpb=ac07859006686a2c62bcf57b24742eb610bc46f0;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 0cbdfbe..eaa685d 100755 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,671 +1,1259 @@ -package jalview.gui; - -import jalview.jbgui.GAlignmentPanel; -import jalview.schemes.*; -import jalview.analysis.*; -import jalview.datamodel.*; -import java.awt.*; -import java.awt.event.*; -import java.awt.print.*; -import java.io.*; -import java.awt.image.*; -import org.jibble.epsgraphics.*; -import javax.imageio.*; - - - -public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable -{ - - AlignViewport av; - OverviewPanel overviewPanel; - SeqPanel seqPanel; - IdPanel idPanel; - IdwidthAdjuster idwidthAdjuster; - public AlignFrame alignFrame; - ScalePanel scalePanel; - AnnotationPanel annotationPanel; - AnnotationLabels alabels; - - // this value is set false when selection area being dragged - boolean fastPaint = true; - - 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); - - Dimension d = calculateIdWidth(); - d.setSize( d.width+4, d.height); - idPanel.idCanvas.setPreferredSize( d ); - hscrollFillerPanel.setPreferredSize( d ); - - scalePanelHolder.add(scalePanel, BorderLayout.CENTER); - seqPanelHolder.add(seqPanel, BorderLayout.CENTER); - - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - public void run() - { - invalidate(); - setScrollValues(0,0); - Dimension d = calculateIdWidth(); - d.setSize( d.width+4, d.height); - idPanel.idCanvas.setPreferredSize( d ); - RefreshPanels(); - } - }); - - - hscroll.addAdjustmentListener(this); - vscroll.addAdjustmentListener(this); - - addComponentListener(new ComponentAdapter() - { - public void componentResized(ComponentEvent evt) - { - RefreshPanels(); - } - }); - - setFocusable(true); - addKeyListener(new KeyAdapter() - { - public void keyPressed(KeyEvent evt) - { - switch(evt.getKeyCode()) - { - case 27: // escape key - av.setSelectionGroup(null); - RefreshPanels(); - break; - case KeyEvent.VK_X: - if(evt.isControlDown()) - alignFrame.cut_actionPerformed(null); - break; - case KeyEvent.VK_C: - if(evt.isControlDown()) - alignFrame.copy_actionPerformed(null); - break; - case KeyEvent.VK_V: - if(evt.isControlDown()) - alignFrame.paste(true); - break; - case KeyEvent.VK_A: - if(evt.isControlDown()) - alignFrame.selectAllSequenceMenuItem_actionPerformed(null); - break; - case KeyEvent.VK_DOWN: - alignFrame.moveSelectedSequences(false); - break; - case KeyEvent.VK_UP: - alignFrame.moveSelectedSequences(true); - break; - case KeyEvent.VK_F: - if(evt.isControlDown()) - alignFrame.findMenuItem_actionPerformed(null); - break; - } - } - }); - } - - Dimension calculateIdWidth() - { - Graphics g = this.getGraphics(); - if(g==null) - { - javax.swing.JFrame f = new javax.swing.JFrame(); - f.addNotify(); - g = f.getGraphics(); - } - - FontMetrics fm = g.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); - if(av.getShowFullId()) - id = s.getDisplayId(); - else - id = s.getName(); - - if (fm.stringWidth(id) > idWidth) - idWidth = fm.stringWidth(id); - i++; - } - - // Also check annotation label widths - i=0; - if(al.getAlignmentAnnotation()!=null) - { - fm = g.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); - } - - - 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()= av.getAlignment().getHeight()) - return false; - fastPaint = false; - vscroll.setValue(vscroll.getValue() + 1); - } - fastPaint = true; - return true; - } - - 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; - } - - - public void setScrollValues(int x, int y) - { - 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() ); - - } - - - 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(); - - if(av.getWrapAlignment() || !fastPaint) - repaint(); - else - { - seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX, - av.getStartSeq() - oldY); - idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY); - scalePanel.repaint(); - if (av.getShowAnnotation()) - annotationPanel.fastPaint(av.getStartRes() - oldX); - } - - } - - 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); - } - - public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException - { - - int idWidth = calculateIdWidth().width + 4; - - - 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 - 30)/av.getCharHeight())-1; - int pagesWide = av.getAlignment().getWidth() / totalRes +1; - int pagesHigh = av.getAlignment().getHeight() / totalSeq +1; - - if (pi >= pagesWide*pagesHigh) - return Printable.NO_SUCH_PAGE; - - ///////////////////////////// - /// 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; - if(endSeq > av.getAlignment().getHeight()) - endSeq = av.getAlignment().getHeight(); - - - //////////////// - //draw Scale - pg.translate(idWidth,0); - scalePanel.drawScale(pg, startRes, endRes, pwidth-idWidth); - - pg.translate(-idWidth, 30); - //////////////// - // Draw the ids - Color currentColor=null; - Color currentTextColor=null; - for(int i=startSeq; i totalChunks ) - return Printable.NO_SUCH_PAGE; - - //////////////// - // Draw the ids - pg.setClip(0,0,pwidth, noChunksOnPage*chunkHeight); - - pg.setColor(Color.black); - - int rowSize = av.getEndRes() - av.getStartRes(); - // Draw the rest of the panels - - for(int ypos=2*av.charHeight, row=av.getEndRes(); row 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); + } + + /** + * DOCUMENT ME! + * + * @param results + * DOCUMENT ME! + */ + 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 void scrollToPosition(SearchResults results) { + 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) + */ + public void scrollToPosition(SearchResults results, boolean redrawOverview) { + // do we need to scroll the panel? + if (results != null && results.getSize()>0) + { + int seqIndex = av.alignment.findIndex(results); + if (seqIndex==-1) + { + return; + } + SequenceI seq = av.alignment.getSequenceAt(seqIndex); + int [] r = results.getResults(seq, seq.getStart(), seq.getEnd()); + if (r==null) + { + return; + } + int start = r[0]; + int end = r[1]; + if (start<0) + { + return; + } + if (end==seq.getEnd()) + { + return; + } + if (!av.wrapAlignment) + { + if ((av.getStartRes() >= start) + || (av.getEndRes() <= end)) + { + setScrollValues(start-1, seqIndex); + } else if ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)) + { + setScrollValues(av.getStartRes(), seqIndex); + } + } + else + { + scrollToWrappedVisible(start); + } + } + if (!redrawOverview && overviewPanel!=null) + { + overviewPanel.setBoxPosition(); + } + paintAlignment(!redrawOverview); + } + + 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; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setAnnotationVisible(boolean b) + { + if (!av.wrapAlignment) + { + annotationSpaceFillerHolder.setVisible(b); + annotationScroller.setVisible(b); + } + repaint(); + } + + 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"); + } + + int height = annotationPanel.adjustPanelHeight(); + + if (hscroll.isVisible()) + { + height += hscroll.getPreferredSize().height; + } + if (height > alignFrame.getHeight() / 2) + { + height = alignFrame.getHeight() / 2; + } + + hscroll.addNotify(); + + annotationScroller.setPreferredSize(new Dimension(annotationScroller + .getWidth(), height)); + + annotationSpaceFillerHolder.setPreferredSize(new Dimension( + annotationSpaceFillerHolder.getWidth(), height)); + annotationScroller.validate();// repaint(); + 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) + { + 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) + { + jalview.structure.StructureSelectionManager + .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")) + { + 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; + } +}