X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=190682941a129aca2ff76b5377fa7860c4c803a1;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=836d96297a3b973ec3664a3e04306c64fa2346e6;hpb=fbff67c88fe2688da201fd2cf74679425c5bf11e;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java old mode 100755 new mode 100644 index 836d962..1906829 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,1204 +1,1802 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 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 java.beans.*; -import java.io.*; - -import java.awt.*; -import java.awt.event.*; -import java.awt.print.*; -import javax.swing.*; - -import jalview.datamodel.*; -import jalview.jbgui.*; -import jalview.schemes.*; - -/** - * 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); - - 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(); - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - 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 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(SearchResults results) - { - seqPanel.seqCanvas.highlightSearchResults(results); - - // do we need to scroll the panel? - if (results != null) - { - SequenceI seq = results.getResultSequence(0); - int seqIndex = av.alignment.findIndex(seq); - int start = seq.findIndex(results.getResultStart(0)) - 1; - int end = seq.findIndex(results.getResultEnd(0)) - 1; - - if (!av.wrapAlignment) - { - if ( (av.getStartRes() > end) || (av.getEndRes() < start) || - ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex))) - { - setScrollValues(start, seqIndex); - } - } - else - { - scrollToWrappedVisible(start); - } - } - - paintAlignment(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; - } - - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setAnnotationVisible(boolean b) - { - if (!av.wrapAlignment) - { - annotationSpaceFillerHolder.setVisible(b); - annotationScroller.setVisible(b); - } - repaint(); - } - - public void adjustAnnotationHeight() - { - if (alignFrame.getHeight() == 0) - { - System.out.println("NEEDS FIXING"); - } - - int height = annotationPanel.adjustPanelHeight() + - hscroll.getPreferredSize().height; - - if (height > alignFrame.getHeight() / 2) - { - height = alignFrame.getHeight() / 2; - } - - hscroll.addNotify(); - - annotationScroller.setPreferredSize( - new Dimension(annotationScroller.getWidth(), - height + hscroll.getHeight())); - - - annotationSpaceFillerHolder.setPreferredSize(new Dimension( - annotationSpaceFillerHolder.getWidth(), - height)); - - 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) - { - - 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) + 30; - 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) - { - 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 = 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; - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.gui; + +import jalview.analysis.AnnotationSorter; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +import jalview.bin.Cache; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SearchResults; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.jbgui.GAlignmentPanel; +import jalview.math.AlignmentDimension; +import jalview.schemes.ResidueProperties; +import jalview.structure.StructureSelectionManager; +import jalview.util.MessageManager; +import jalview.util.Platform; + +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Container; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Graphics; +import java.awt.Insets; +import java.awt.event.AdjustmentEvent; +import java.awt.event.AdjustmentListener; +import java.awt.print.PageFormat; +import java.awt.print.Printable; +import java.awt.print.PrinterException; +import java.beans.PropertyChangeEvent; +import java.beans.PropertyChangeListener; +import java.io.File; +import java.io.FileWriter; +import java.io.PrintWriter; +import java.util.List; + +import javax.swing.SwingUtilities; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision: 1.161 $ + */ +public class AlignmentPanel extends GAlignmentPanel implements + AdjustmentListener, Printable, AlignmentViewPanel +{ + public AlignViewport av; + + OverviewPanel overviewPanel; + + private SeqPanel seqPanel; + + private IdPanel idPanel; + + private boolean headless; + + IdwidthAdjuster idwidthAdjuster; + + /** DOCUMENT ME!! */ + public AlignFrame alignFrame; + + private ScalePanel scalePanel; + + private AnnotationPanel annotationPanel; + + private AnnotationLabels alabels; + + // this value is set false when selection area being dragged + boolean fastPaint = true; + + int hextent = 0; + + int vextent = 0; + + /* + * Flag set while scrolling to follow complementary cDNA/protein scroll. When + * true, suppresses invoking the same method recursively. + */ + private boolean followingComplementScroll; + + /** + * Creates a new AlignmentPanel object. + * + * @param af + * @param av + */ + public AlignmentPanel(AlignFrame af, final AlignViewport av) + { + alignFrame = af; + this.av = av; + setSeqPanel(new SeqPanel(av, this)); + setIdPanel(new IdPanel(av, this)); + + setScalePanel(new ScalePanel(av, this)); + + idPanelHolder.add(getIdPanel(), BorderLayout.CENTER); + idwidthAdjuster = new IdwidthAdjuster(this); + idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER); + + setAnnotationPanel(new AnnotationPanel(this)); + setAlabels(new AnnotationLabels(this)); + + annotationScroller.setViewportView(getAnnotationPanel()); + annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER); + + scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER); + seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER); + + setScrollValues(0, 0); + + 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(); + updateLayout(); + } + + @Override + public AlignViewportI getAlignViewport() + { + return av; + } + + 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.getCharHeight() + + fm.getDescent())); + idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av + .getCharHeight() + fm.getDescent())); + + getIdPanel().getIdCanvas().gg = null; + getSeqPanel().seqCanvas.img = null; + getAnnotationPanel().adjustPanelHeight(); + + Dimension d = calculateIdWidth(); + + d.setSize(d.width + 4, d.height); + getIdPanel().getIdCanvas().setPreferredSize(d); + hscrollFillerPanel.setPreferredSize(d); + + if (overviewPanel != null) + { + overviewPanel.setBoxPosition(); + } + if (this.alignFrame.getSplitViewContainer() != null) + { + ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout(); + } + + repaint(); + } + + /** + * Calculate the width of the alignment labels based on the displayed names + * and any bounds on label width set in preferences. + * + * @return Dimension giving the maximum width of the alignment label panel + * that should be used. + */ + public Dimension calculateIdWidth() + { + // calculate sensible default width when no preference is available + Dimension r = null; + if (av.getIdWidth() < 0) + { + int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300); + int maxwidth = Math.max(20, Math.min(afwidth - 200, 2 * afwidth / 3)); + r = calculateIdWidth(maxwidth); + av.setIdWidth(r.width); + } + else + { + r = new Dimension(); + r.width = av.getIdWidth(); + r.height = 0; + } + return r; + } + + /** + * Calculate the width of the alignment labels based on the displayed names + * and any bounds on label width set in preferences. + * + * @param maxwidth + * -1 or maximum width allowed for IdWidth + * @return Dimension giving the maximum width of the alignment label panel + * that should be used. + */ + public Dimension calculateIdWidth(int maxwidth) + { + Container c = new Container(); + + FontMetrics fm = c.getFontMetrics(new Font(av.font.getName(), + Font.ITALIC, av.font.getSize())); + + AlignmentI al = av.getAlignment(); + int i = 0; + int idWidth = 0; + String id; + + while ((i < al.getHeight()) && (al.getSequenceAt(i) != null)) + { + SequenceI s = al.getSequenceAt(i); + + id = s.getDisplayId(av.getShowJVSuffix()); + + if (fm.stringWidth(id) > idWidth) + { + idWidth = fm.stringWidth(id); + } + + i++; + } + + // Also check annotation label widths + i = 0; + + if (al.getAlignmentAnnotation() != null) + { + fm = c.getFontMetrics(getAlabels().getFont()); + + while (i < al.getAlignmentAnnotation().length) + { + String label = al.getAlignmentAnnotation()[i].label; + + if (fm.stringWidth(label) > idWidth) + { + idWidth = fm.stringWidth(label); + } + + i++; + } + } + + return new Dimension(maxwidth < 0 ? idWidth : Math.min(maxwidth, + idWidth), 12); + } + + /** + * Highlight the given results on the alignment. + * + */ + public void highlightSearchResults(SearchResults results) + { + scrollToPosition(results); + getSeqPanel().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, 0, true, false); + } + + /** + * Scroll the view to show the position of the highlighted region in results + * (if any) + * + * @param searchResults + * @param redrawOverview + * @return + */ + public boolean scrollToPosition(SearchResults searchResults, + boolean redrawOverview) + { + return scrollToPosition(searchResults, 0, redrawOverview, false); + } + + /** + * Scroll the view to show the position of the highlighted region in results + * (if any) + * + * @param results + * @param verticalOffset + * if greater than zero, allows scrolling to a position below the + * first displayed sequence + * @param redrawOverview + * - when set, the overview will be recalculated (takes longer) + * @param centre + * if true, try to centre the search results horizontally in the view + * @return false if results were not found + */ + public boolean scrollToPosition(SearchResults results, + int verticalOffset, boolean redrawOverview, boolean centre) + { + int startv, endv, starts, ends; + // 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 nullpointerexceptions raised here. + if (results != null && results.getSize() > 0 && av != null + && av.getAlignment() != null) + { + int seqIndex = av.getAlignment().findIndex(results); + if (seqIndex == -1) + { + return false; + } + SequenceI seq = av.getAlignment().getSequenceAt(seqIndex); + + int[] r = results.getResults(seq, 0, av.getAlignment().getWidth()); + if (r == null) + { + return false; + } + int start = r[0]; + int end = r[1]; + // DEBUG + // System.err.println(this.av.viewName + " Seq : " + seqIndex + // + " Scroll to " + start + "," + end); + + /* + * To centre results, scroll to positions half the visible width + * left/right of the start/end positions + */ + if (centre) + { + int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1; + start = Math.max(start - offset, 0); + end = end + offset - 1; + } + if (start < 0) + { + return false; + } + if (end == seq.getEnd()) + { + return false; + } + if (av.hasHiddenColumns()) + { + start = av.getColumnSelection().findColumnPosition(start); + end = av.getColumnSelection().findColumnPosition(end); + if (start == end) + { + if (!av.getColumnSelection().isVisible(r[0])) + { + // don't scroll - position isn't visible + return false; + } + } + } + + /* + * allow for offset of target sequence (actually scroll to one above it) + */ + seqIndex = Math.max(0, seqIndex - verticalOffset); + + // System.out.println("start=" + start + ", end=" + end + ", startv=" + // + av.getStartRes() + ", endv=" + av.getEndRes() + ", starts=" + // + av.getStartSeq() + ", ends=" + av.getEndSeq()); + if (!av.getWrapAlignment()) + { + if ((startv = av.getStartRes()) >= start) + { + /* + * Scroll left to make start of search results visible + */ + // setScrollValues(start - 1, seqIndex); // plus one residue + setScrollValues(start, seqIndex); + } + else if ((endv = av.getEndRes()) <= end) + { + /* + * Scroll right to make end of search results visible + */ + // setScrollValues(startv + 1 + end - endv, seqIndex); // plus one + setScrollValues(startv + end - endv, seqIndex); + } + else if ((starts = av.getStartSeq()) > seqIndex) + { + /* + * Scroll up to make start of search results visible + */ + setScrollValues(av.getStartRes(), seqIndex); + } + else if ((ends = av.getEndSeq()) <= seqIndex) + { + /* + * Scroll down to make end of search results visible + */ + setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); + } + /* + * Else results are already visible - no need to scroll + */ + } + else + { + scrollToWrappedVisible(start); + } + } + if (redrawOverview && overviewPanel != null) + { + overviewPanel.setBoxPosition(); + } + paintAlignment(redrawOverview); + return true; + } + + void scrollToWrappedVisible(int res) + { + int cwidth = getSeqPanel().seqCanvas + .getWrappedCanvasWidth(getSeqPanel().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.getWrapAlignment()) + { + 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 annotationHeight = getAnnotationPanel().adjustPanelHeight(); + + if (adjustPanelHeight) + { + int rowHeight = av.getCharHeight(); + int alignmentHeight = rowHeight * av.getAlignment().getHeight(); + + /* + * Estimate available height in the AlignFrame for alignment + + * annotations. Deduct an estimate for title bar, menu bar, scale panel, + * hscroll, status bar (as these are not laid out we can't inspect their + * actual heights). Insets gives frame borders. + */ + int stuff = Platform.isAMac() ? 80 : 100; + Insets insets = alignFrame.getInsets(); + int availableHeight = alignFrame.getHeight() - stuff - insets.top + - insets.bottom; + + /* + * If not enough vertical space, maximize annotation height while keeping + * at least two rows of alignment visible + */ + if (annotationHeight + alignmentHeight > availableHeight) + { + annotationHeight = Math.min(annotationHeight, availableHeight - 2 + * rowHeight); + } + } + else + { + // maintain same window layout whilst updating sliders + annotationHeight = annotationScroller.getSize().height; + } + hscroll.addNotify(); + + annotationScroller.setPreferredSize(new Dimension(annotationScroller + .getWidth(), annotationHeight)); + + annotationSpaceFillerHolder.setPreferredSize(new Dimension( + annotationSpaceFillerHolder.getWidth(), annotationHeight)); + annotationScroller.validate(); + annotationScroller.addNotify(); + } + + /** + * update alignment layout for viewport settings + * + * @param wrap + * DOCUMENT ME! + */ + public void updateLayout() + { + fontChanged(); + setAnnotationVisible(av.isShowAnnotation()); + boolean wrap = av.getWrapAlignment(); + av.startSeq = 0; + scalePanelHolder.setVisible(!wrap); + hscroll.setVisible(!wrap); + idwidthAdjuster.setVisible(!wrap); + + if (wrap) + { + annotationScroller.setVisible(false); + annotationSpaceFillerHolder.setVisible(false); + } + else if (av.isShowAnnotation()) + { + annotationScroller.setVisible(true); + annotationSpaceFillerHolder.setVisible(true); + } + + 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 + * @param y + * visible row to scroll to + * + */ + public void setScrollValues(int x, int y) + { + // System.err.println("Scroll " + this.av.viewName + " to " + x + "," + y); + if (av == null || av.getAlignment() == null) + { + return; + } + int width = av.getAlignment().getWidth(); + int height = av.getAlignment().getHeight(); + + if (av.hasHiddenColumns()) + { + width = av.getColumnSelection().findColumnPosition(width); + } + + av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av + .getCharWidth())) - 1); + + hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); + vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); + + if (hextent > width) + { + hextent = width; + } + + if (vextent > height) + { + vextent = height; + } + + if ((hextent + x) > width) + { + x = width - hextent; + } + + if ((vextent + y) > height) + { + y = height - vextent; + } + + if (y < 0) + { + y = 0; + } + + if (x < 0) + { + x = 0; + } + + 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 + (getSeqPanel().seqCanvas.getWidth() / av + .getCharWidth())) - 1); + } + + if (evt.getSource() == vscroll) + { + int offy = vscroll.getValue(); + + if (av.getWrapAlignment()) + { + if (offy > -1) + { + int rowSize = getSeqPanel().seqCanvas + .getWrappedCanvasWidth(getSeqPanel().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 + + (getSeqPanel().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) + { + getIdPanel().getIdCanvas().fastPaint(scrollY); + getSeqPanel().seqCanvas.fastPaint(scrollX, scrollY); + getScalePanel().repaint(); + + if (av.isShowAnnotation() && scrollX != 0) + { + getAnnotationPanel().fastPaint(scrollX); + } + } + } + /* + * If there is one, scroll the (Protein/cDNA) complementary alignment to + * match, unless we are ourselves doing that. + */ + if (isFollowingComplementScroll()) + { + setFollowingComplementScroll(false); + } + else + { + av.scrollComplementaryAlignment(); + } + } + + /** + * Repaint the alignment including the annotations and overview panels (if + * shown). + */ + public void paintAlignment(boolean updateOverview) + { + final AnnotationSorter sorter = new AnnotationSorter(getAlignment(), + av.isShowAutocalculatedAbove()); + sorter.sort(getAlignment().getAlignmentAnnotation(), + av.getSortAnnotationsBy()); + repaint(); + + if (updateOverview) + { + // TODO: determine if this paintAlignment changed structure colours + av.getStructureSelectionManager().sequenceColoursChanged(this); + + if (overviewPanel != null) + { + overviewPanel.updateOverviewImage(); + } + } + } + + /** + * DOCUMENT ME! + * + * @param g + * DOCUMENT ME! + */ + public void paintComponent(Graphics g) + { + invalidate(); + + Dimension d = getIdPanel().getIdCanvas().getPreferredSize(); + idPanelHolder.setPreferredSize(d); + hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12)); + validate(); + + if (av.getWrapAlignment()) + { + int maxwidth = av.getAlignment().getWidth(); + + if (av.hasHiddenColumns()) + { + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + } + + int canvasWidth = getSeqPanel().seqCanvas + .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth()); + if (canvasWidth > 0) + { + int max = maxwidth + / getSeqPanel().seqCanvas + .getWrappedCanvasWidth(getSeqPanel().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(false); + FontMetrics fm = getFontMetrics(av.getFont()); + int scaleHeight = av.getCharHeight() + 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 = (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.getAlignment().getHeight() / totalSeq) + 1) + * pheight; + + if (av.isShowAnnotation()) + { + pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3; + } + + pagesHigh /= pheight; + + if (pi >= (pagesWide * pagesHigh)) + { + return Printable.NO_SUCH_PAGE; + } + + // draw Scale + pg.translate(idWidth, 0); + getScalePanel().drawScale(pg, startRes, endRes, pwidth - idWidth, + scaleHeight); + pg.translate(-idWidth, scaleHeight); + + // ////////////// + // Draw the ids + Color currentColor = null; + Color currentTextColor = null; + + pg.setFont(getIdPanel().getIdCanvas().getIdfont()); + + 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.getCharHeight(), idWidth, + av.getCharHeight()); + + pg.setColor(currentTextColor); + + int xPos = 0; + if (av.isRightAlignIds()) + { + fm = pg.getFontMetrics(); + xPos = idWidth + - fm.stringWidth(seq.getDisplayId(av.getShowJVSuffix())) + - 4; + } + + pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos, + (((i - startSeq) * av.getCharHeight()) + av.getCharHeight()) + - (av.getCharHeight() / 5)); + } + + pg.setFont(av.getFont()); + + // draw main sequence panel + pg.translate(idWidth, 0); + getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq, + endSeq, 0); + + if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight())) + { + // draw annotation - need to offset for current scroll position + int offset = -getAlabels().getScrollOffset(); + pg.translate(0, offset); + pg.translate(-idWidth - 3, (endSeq - startSeq) * av.getCharHeight() + + 3); + getAlabels().drawComponent(pg, idWidth); + pg.translate(idWidth + 3, 0); + getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av, + pg, -1, startRes, endRes + 1); + pg.translate(0, -offset); + } + + 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.isShowAnnotation()) + { + annotationHeight = getAnnotationPanel().adjustPanelHeight(); + labels = new AnnotationLabels(av); + } + + int hgap = av.getCharHeight(); + if (av.getScaleAboveWrapped()) + { + hgap += av.getCharHeight(); + } + + int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap + + annotationHeight; + + int idWidth = getVisibleIdWidth(false); + + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) + { + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + } + + int resWidth = getSeqPanel().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.getAlignment().getHeight(); i++) + { + pg.setFont(getIdPanel().getIdCanvas().getIdfont()); + SequenceI s = av.getAlignment().getSequenceAt(i); + String string = s.getDisplayId(av.getShowJVSuffix()); + int xPos = 0; + if (av.isRightAlignIds()) + { + FontMetrics fm = pg.getFontMetrics(); + xPos = idWidth - fm.stringWidth(string) - 4; + } + pg.drawString(string, xPos, + ((i * av.getCharHeight()) + ypos + av.getCharHeight()) + - (av.getCharHeight() / 5)); + } + if (labels != null) + { + pg.translate(-3, + ypos + (av.getAlignment().getHeight() * av.getCharHeight())); + + pg.setFont(av.getFont()); + labels.drawComponent(pg, idWidth); + pg.translate( + +3, + -ypos + - (av.getAlignment().getHeight() * av + .getCharHeight())); + } + + ypos += cHeight; + } while (ypos < totalHeight); + + pg.translate(idWidth, 0); + + getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, + totalHeight, 0); + + if ((pi * pheight) < totalHeight) + { + return Printable.PAGE_EXISTS; + + } + else + { + return Printable.NO_SUCH_PAGE; + } + } + + /** + * get current sequence ID panel width, or nominal value if panel were to be + * displayed using default settings + * + * @return + */ + public int getVisibleIdWidth() + { + return getVisibleIdWidth(true); + } + + /** + * get current sequence ID panel width, or nominal value if panel were to be + * displayed using default settings + * + * @param onscreen + * indicate if the Id width for onscreen or offscreen display should + * be returned + * @return + */ + public int getVisibleIdWidth(boolean onscreen) + { + // see if rendering offscreen - check preferences and calc width accordingly + if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false)) + { + return calculateIdWidth(-1).width + 4; + } + Integer idwidth = null; + if (onscreen + || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null) + { + return (getIdPanel().getWidth() > 0 ? getIdPanel().getWidth() + : calculateIdWidth().width + 4); + } + return idwidth.intValue() + 4; + } + + void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file) + { + long progress = System.currentTimeMillis(); + headless = (System.getProperty("java.awt.headless") != null && System + .getProperty("java.awt.headless").equals("true")); + if (alignFrame != null && !headless) + { + alignFrame.setProgressBar(MessageManager.formatMessage( + "status.saving_file", new Object[] { type.getLabel() }), + progress); + } + try + { + AlignmentDimension aDimension = getAlignmentDimension(); + try + { + jalview.util.ImageMaker im; + final String imageAction, imageTitle; + if (type == jalview.util.ImageMaker.TYPE.PNG) + { + imageAction = "Create PNG image from alignment"; + imageTitle = null; + } + else if (type == jalview.util.ImageMaker.TYPE.EPS) + { + imageAction = "Create EPS file from alignment"; + imageTitle = alignFrame.getTitle(); + } + else + { + imageAction = "Create SVG file from alignment"; + imageTitle = alignFrame.getTitle(); + } + + im = new jalview.util.ImageMaker(this, type, imageAction, + aDimension.getWidth(), aDimension.getHeight(), file, + imageTitle); + if (av.getWrapAlignment()) + { + if (im.getGraphics() != null) + { + printWrappedAlignment(im.getGraphics(), aDimension.getWidth(), + aDimension.getHeight(), 0); + im.writeImage(); + } + } + else + { + if (im.getGraphics() != null) + { + printUnwrapped(im.getGraphics(), aDimension.getWidth(), + aDimension.getHeight(), 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(); + } + } finally + { + if (alignFrame != null && !headless) + { + alignFrame.setProgressBar( + MessageManager.getString("status.export_complete"), + progress); + } + } + } + + public AlignmentDimension getAlignmentDimension() + { + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) + { + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth); + } + + int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight()) + + getScalePanel().getHeight(); + int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth()); + + if (av.getWrapAlignment()) + { + height = getWrappedHeight(); + if (headless) + { + // need to obtain default alignment width and then add in any + // additional allowance for id margin + // this duplicates the calculation in getWrappedHeight but adjusts for + // offscreen idWith + width = alignFrame.getWidth() - vscroll.getPreferredSize().width + - alignFrame.getInsets().left + - alignFrame.getInsets().right - getVisibleIdWidth() + + getVisibleIdWidth(false); + } + else + { + width = getSeqPanel().getWidth() + getVisibleIdWidth(false); + } + + } + else if (av.isShowAnnotation()) + { + height += getAnnotationPanel().adjustPanelHeight() + 3; + } + return new AlignmentDimension(width, height); + + } + + /** + * DOCUMENT ME! + */ + public void makeEPS(File epsFile) + { + makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile); + } + + /** + * DOCUMENT ME! + */ + public void makePNG(File pngFile) + { + makeAlignmentImage(jalview.util.ImageMaker.TYPE.PNG, pngFile); + } + + public void makeSVG(File svgFile) + { + makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile); + } + + public void makePNGImageMap(File imgMapFile, String imageName) + { + // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS + // //////////////////////////////////////////// + int idWidth = getVisibleIdWidth(false); + FontMetrics fm = getFontMetrics(av.getFont()); + int scaleHeight = av.getCharHeight() + fm.getDescent(); + + // Gen image map + // //////////////////////////////// + if (imgMapFile != null) + { + try + { + int s, sSize = av.getAlignment().getHeight(), res, alwidth = av + .getAlignment().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.getCharHeight() + scaleHeight; + + SequenceI seq = av.getAlignment().getSequenceAt(s); + SequenceFeature[] features = seq.getSequenceFeatures(); + SequenceGroup[] groups = av.getAlignment().findAllGroups(seq); + for (res = 0; res < alwidth; res++) + { + text = new StringBuffer(); + String triplet = null; + if (av.getAlignment().isNucleotide()) + { + triplet = ResidueProperties.nucleotideName.get(seq + .getCharAt(res) + ""); + } + else + { + triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(res) + + ""); + } + + if (triplet == null) + { + continue; + } + + 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 = getSeqPanel().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 = getSeqPanel().seqCanvas + .getWrappedCanvasWidth(seqPanelWidth); + + int hgap = av.getCharHeight(); + if (av.getScaleAboveWrapped()) + { + hgap += av.getCharHeight(); + } + + int annotationHeight = 0; + if (av.isShowAnnotation()) + { + annotationHeight = getAnnotationPanel().adjustPanelHeight(); + } + + int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap + + annotationHeight; + + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) + { + maxwidth = av.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(getSeqPanel().seqCanvas); + PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas()); + PaintRefresher.RemoveComponent(this); + if (av != null) + { + jalview.structure.StructureSelectionManager ssm = av + .getStructureSelectionManager(); + ssm.removeStructureViewerListener(getSeqPanel(), null); + ssm.removeSelectionListener(getSeqPanel()); + ssm.removeCommandListener(av); + ssm.removeStructureViewerListener(getSeqPanel(), null); + ssm.removeSelectionListener(getSeqPanel()); + av.setAlignment(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, false); + } + + public void updateAnnotation(boolean applyGlobalSettings) + { + updateAnnotation(applyGlobalSettings, false); + } + + public void updateAnnotation(boolean applyGlobalSettings, + boolean preserveNewGroupSettings) + { + av.updateGroupAnnotationSettings(applyGlobalSettings, + preserveNewGroupSettings); + adjustAnnotationHeight(); + } + + @Override + public AlignmentI getAlignment() + { + return av == null ? null : av.getAlignment(); + } + + @Override + public String getViewName() + { + return av.viewName; + } + + /** + * Make/Unmake this alignment panel the current input focus + * + * @param b + */ + public void setSelected(boolean b) + { + try + { + if (alignFrame.getSplitViewContainer() != null) + { + /* + * bring enclosing SplitFrame to front first if there is one + */ + ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b); + } + alignFrame.setSelected(b); + } catch (Exception ex) + { + } + + if (b) + { + alignFrame.setDisplayedView(this); + } + } + + @Override + public StructureSelectionManager getStructureSelectionManager() + { + return av.getStructureSelectionManager(); + } + + @Override + public void raiseOOMWarning(String string, OutOfMemoryError error) + { + new OOMWarning(string, error, this); + } + + @Override + public jalview.api.FeatureRenderer cloneFeatureRenderer() + { + + return new FeatureRenderer(this); + } + + @Override + public jalview.api.FeatureRenderer getFeatureRenderer() + { + return seqPanel.seqCanvas.getFeatureRenderer(); + } + + public void updateFeatureRenderer( + jalview.renderer.seqfeatures.FeatureRenderer fr) + { + fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer()); + } + + public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr) + { + if (getSeqPanel().seqCanvas.getFeatureRenderer() != null) + { + getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr); + } + } + + public ScalePanel getScalePanel() + { + return scalePanel; + } + + public void setScalePanel(ScalePanel scalePanel) + { + this.scalePanel = scalePanel; + } + + public SeqPanel getSeqPanel() + { + return seqPanel; + } + + public void setSeqPanel(SeqPanel seqPanel) + { + this.seqPanel = seqPanel; + } + + public AnnotationPanel getAnnotationPanel() + { + return annotationPanel; + } + + public void setAnnotationPanel(AnnotationPanel annotationPanel) + { + this.annotationPanel = annotationPanel; + } + + public AnnotationLabels getAlabels() + { + return alabels; + } + + public void setAlabels(AnnotationLabels alabels) + { + this.alabels = alabels; + } + + public IdPanel getIdPanel() + { + return idPanel; + } + + public void setIdPanel(IdPanel idPanel) + { + this.idPanel = idPanel; + } + + /** + * Follow a scrolling change in the (cDNA/Protein) complementary alignment. + * The aim is to keep the two alignments 'lined up' on their centre columns. + * + * @param sr + * holds mapped region(s) of this alignment that we are scrolling + * 'to'; may be modified for sequence offset by this method + * @param verticalOffset + * the number of visible sequences to show above the mapped region + */ + public void scrollToCentre(SearchResults sr, int verticalOffset) + { + /* + * To avoid jumpy vertical scrolling (if some sequences are gapped or not + * mapped), we can make the scroll-to location a sequence above the one + * actually mapped. + */ + SequenceI mappedTo = sr.getResultSequence(0); + List seqs = av.getAlignment().getSequences(); + + /* + * This is like AlignmentI.findIndex(seq) but here we are matching the + * dataset sequence not the aligned sequence + */ + boolean matched = false; + for (SequenceI seq : seqs) + { + if (mappedTo == seq.getDatasetSequence()) + { + matched = true; + break; + } + } + if (!matched) + { + return; // failsafe, shouldn't happen + } + + /* + * Scroll to position but centring the target residue. + */ + scrollToPosition(sr, verticalOffset, true, true); + } + + /** + * Set a flag to say we are scrolling to follow a (cDNA/protein) complement. + * + * @param b + */ + protected void setFollowingComplementScroll(boolean b) + { + this.followingComplementScroll = b; + } + + protected boolean isFollowingComplementScroll() + { + return this.followingComplementScroll; + } +}