X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=c3ebd7153f026eaeb325d5e66f268dd1cf7b81b7;hb=d1a58585358deed317674daeeac5fb5be66637ab;hp=1a48af6fbe1471e03fd96d4fbbb6dc0825674cb5;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 1a48af6..c3ebd71 100755 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2006 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 @@ -18,29 +18,37 @@ */ package jalview.gui; -import java.io.*; -import javax.imageio.*; +import jalview.datamodel.*; + +import jalview.jbgui.*; + +import jalview.schemes.*; import java.awt.*; import java.awt.event.*; -import java.awt.image.*; import java.awt.print.*; + +import java.io.*; + import javax.swing.*; -import org.jibble.epsgraphics.*; -import jalview.analysis.*; -import jalview.datamodel.*; -import jalview.jbgui.*; -import jalview.schemes.*; -public class AlignmentPanel - extends GAlignmentPanel implements AdjustmentListener, Printable +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class AlignmentPanel extends GAlignmentPanel + implements AdjustmentListener, Printable { - AlignViewport av; + public AlignViewport av; OverviewPanel overviewPanel; SeqPanel seqPanel; IdPanel idPanel; IdwidthAdjuster idwidthAdjuster; + + /** DOCUMENT ME!! */ public AlignFrame alignFrame; ScalePanel scalePanel; AnnotationPanel annotationPanel; @@ -51,6 +59,12 @@ public class AlignmentPanel 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; @@ -67,49 +81,30 @@ public class AlignmentPanel annotationPanel = new AnnotationPanel(this); alabels = new AnnotationLabels(this); - annotationSpaceFillerHolder.setPreferredSize(annotationPanel. - getPreferredSize()); - annotationScroller.setPreferredSize(annotationPanel.getPreferredSize()); annotationScroller.setViewportView(annotationPanel); annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER); fontChanged(); scalePanelHolder.add(scalePanel, BorderLayout.CENTER); - seqPanelHolder.add(seqPanel, BorderLayout.CENTER); + seqPanelHolder.add(seqPanel, BorderLayout.CENTER); setScrollValues(0, 0); + setAnnotationVisible(av.getShowAnnotation()); + hscroll.addAdjustmentListener(this); vscroll.addAdjustmentListener(this); - setFocusable(true); - addKeyListener(new KeyAdapter() - { - public void keyPressed(KeyEvent evt) - { - switch (evt.getKeyCode()) - { - case 27: // escape key - av.setSelectionGroup(null); - repaint(); - - break; - - case KeyEvent.VK_DOWN: - alignFrame.moveSelectedSequences(false); - break; + adjustAnnotationHeight(); - case KeyEvent.VK_UP: - alignFrame.moveSelectedSequences(true); - - break; - } - } - }); } + + /** + * DOCUMENT ME! + */ public void fontChanged() { // set idCanvas bufferedImage to null @@ -122,27 +117,32 @@ public class AlignmentPanel 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(); } - Dimension calculateIdWidth() + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public Dimension calculateIdWidth() { - Graphics g = this.getGraphics(); + Container c = new Container(); - if (g == null) - { - javax.swing.JFrame f = new javax.swing.JFrame(); - f.addNotify(); - g = f.getGraphics(); - } + FontMetrics fm = c.getFontMetrics( + new Font(av.font.getName(), Font.ITALIC, av.font.getSize())); - FontMetrics fm = g.getFontMetrics(av.font); AlignmentI al = av.getAlignment(); int i = 0; @@ -153,14 +153,7 @@ public class AlignmentPanel { SequenceI s = al.getSequenceAt(i); - if (av.getShowFullId()) - { - id = s.getDisplayId(); - } - else - { - id = s.getName(); - } + id = s.getDisplayId(av.getShowJVSuffix()); if (fm.stringWidth(id) > idWidth) { @@ -175,7 +168,7 @@ public class AlignmentPanel if (al.getAlignmentAnnotation() != null) { - fm = g.getFontMetrics(alabels.getFont()); + fm = c.getFontMetrics(alabels.getFont()); while (i < al.getAlignmentAnnotation().length) { @@ -193,76 +186,134 @@ public class AlignmentPanel return new Dimension(idWidth, 12); } - public void highlightSearchResults(int[] results) + /** + * 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 = av.alignment.getSequenceAt(results[0]); - int start = seq.findIndex(results[1]) - 1; - int end = seq.findIndex(results[2]) - 1; + 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.getStartRes() > start) || (av.getEndRes() < end) || - ( (av.getStartSeq() > results[0]) || - (av.getEndSeq() < results[0]))) + if(!av.wrapAlignment) { - setScrollValues(start, results[0]); + if ( (av.getStartRes() > end) || (av.getEndRes() < start) || + ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex))) + { + setScrollValues(start, seqIndex); + } + } + else + { + scrollToWrappedVisible(start); } } } + 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) { - annotationSpaceFillerHolder.setVisible(b); - annotationScroller.setVisible(b); + if (!av.wrapAlignment) + { + annotationSpaceFillerHolder.setVisible(b); + annotationScroller.setVisible(b); + } + repaint(); } - public void setWrapAlignment(boolean wrap) + public void adjustAnnotationHeight() { - scalePanelHolder.setVisible(!wrap); - hscroll.setVisible(!wrap); - idwidthAdjuster.setVisible(!wrap); + if (alignFrame.getHeight() == 0) + { + System.out.println("NEEDS FIXING"); + } - av.setShowAnnotation(!wrap); - annotationScroller.setVisible(!wrap); - annotationSpaceFillerHolder.setVisible(!wrap); - idSpaceFillerPanel1.setVisible(!wrap); + int height = annotationPanel.adjustPanelHeight(); + + if (height > alignFrame.getHeight() / 2) + { + height = alignFrame.getHeight() / 2; + } + annotationScroller.setPreferredSize( + new Dimension(annotationScroller.getWidth(), + height)); + + annotationSpaceFillerHolder.setPreferredSize(new Dimension( + annotationSpaceFillerHolder.getWidth(), + height)); + + annotationPanel.repaint(); repaint(); } - public void setColourScheme() + /** + * DOCUMENT ME! + * + * @param wrap DOCUMENT ME! + */ + public void setWrapAlignment(boolean wrap) { - ColourSchemeI cs = av.getGlobalColourScheme(); + av.startSeq = 0; + scalePanelHolder.setVisible(!wrap); + hscroll.setVisible(!wrap); + idwidthAdjuster.setVisible(!wrap); - if (av.getConservationSelected()) + if (wrap) { - Alignment al = (Alignment) av.getAlignment(); - Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, - al.getSequences(), 0, - al.getWidth()); - - c.calculate(); - c.verdict(false, av.ConsPercGaps); - - ConservationColourScheme ccs = new ConservationColourScheme(c, cs); - - av.setGlobalColourScheme(ccs); + annotationScroller.setVisible(false); + annotationSpaceFillerHolder.setVisible(false); + } + else if (av.showAnnotation) + { + annotationScroller.setVisible(true); + annotationSpaceFillerHolder.setVisible(true); } + idSpaceFillerPanel1.setVisible(!wrap); + repaint(); } @@ -295,9 +346,16 @@ public class AlignmentPanel return true; } + /** + * DOCUMENT ME! + * + * @param right DOCUMENT ME! + * + * @return DOCUMENT ME! + */ public boolean scrollRight(boolean right) { - if (right) + if (!right) { if (hscroll.getValue() < 1) { @@ -323,32 +381,44 @@ public class AlignmentPanel return true; } + /** + * DOCUMENT ME! + * + * @param x DOCUMENT ME! + * @param y DOCUMENT ME! + */ public void setScrollValues(int x, int y) { - av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - - 1); + + 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 > av.alignment.getWidth()) + if (hextent > width) { - hextent = av.alignment.getWidth(); + hextent = width; } - if (vextent > av.alignment.getHeight()) + if (vextent > height) { - vextent = av.alignment.getHeight(); + vextent = height; } - if ( (hextent + x) > av.getAlignment().getWidth()) + if ( (hextent + x) > width) { - x = av.getAlignment().getWidth() - hextent; + x = width - hextent; } - if ( (vextent + y) > av.getAlignment().getHeight()) + if ( (vextent + y) > height) { - y = av.getAlignment().getHeight() - vextent; + y = height - vextent; } if (y < 0) @@ -361,12 +431,18 @@ public class AlignmentPanel x = 0; } - hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth()); - vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight()); + 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(); @@ -384,10 +460,26 @@ public class AlignmentPanel if (av.getWrapAlignment()) { - int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel. - seqCanvas.getWidth()); - av.setStartRes(vscroll.getValue() * rowSize); - av.setEndRes( (vscroll.getValue() + 1) * rowSize); + 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 { @@ -402,25 +494,42 @@ public class AlignmentPanel overviewPanel.setBoxPosition(); } + int scrollX = av.startRes - oldX; + int scrollY = av.startSeq - oldY; + if (av.getWrapAlignment() || !fastPaint) { repaint(); } else { - idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY); - seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX, - av.getStartSeq() - oldY); - - scalePanel.repaint(); - - if (av.getShowAnnotation()) + // 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(scrollX0) + { + 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()); } + + if( this.getVisibleRect().getBounds() == g.getClipBounds() + && overviewPanel != null) + overviewPanel.updateOverviewImage(); } + /** + * DOCUMENT ME! + * + * @param pg DOCUMENT ME! + * @param pf DOCUMENT ME! + * @param pi DOCUMENT ME! + * + * @return DOCUMENT ME! + * + * @throws PrinterException DOCUMENT ME! + */ public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException { @@ -462,10 +597,22 @@ public class AlignmentPanel } } + /** + * DOCUMENT ME! + * + * @param pg DOCUMENT ME! + * @param pwidth DOCUMENT ME! + * @param pheight DOCUMENT ME! + * @param pi DOCUMENT ME! + * + * @return DOCUMENT ME! + * + * @throws PrinterException DOCUMENT ME! + */ public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException { - int idWidth = calculateIdWidth().width + 4; + int idWidth = getVisibleIdWidth(); FontMetrics fm = getFontMetrics(av.getFont()); int scaleHeight = av.charHeight + fm.getDescent(); @@ -517,7 +664,7 @@ public class AlignmentPanel if (av.showAnnotation) { - pagesHigh += annotationPanel.getHeight(); + pagesHigh += annotationPanel.adjustPanelHeight() + 3; } pagesHigh /= pheight; @@ -537,10 +684,13 @@ public class AlignmentPanel Color currentColor = null; Color currentTextColor = null; + pg.setFont(new Font(av.getFont().getName(), + Font.ITALIC, + av.getFont().getSize())); for (int i = startSeq; i < endSeq; i++) { if ( (av.getSelectionGroup() != null) && - av.getSelectionGroup().sequences.contains( + av.getSelectionGroup().getSequences(false).contains( av.getAlignment().getSequenceAt(i))) { currentColor = Color.gray; @@ -553,35 +703,30 @@ public class AlignmentPanel } pg.setColor(currentColor); - pg.fillRect(0, - jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, - av.getCharHeight()), idWidth, av.getCharHeight()); + pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth, + av.getCharHeight()); pg.setColor(currentTextColor); - String string = av.getAlignment().getSequenceAt(i).getName(); - - if (av.getShowFullId()) - { - string = av.getAlignment().getSequenceAt(i).getDisplayId(); - } + String string = av.getAlignment().getSequenceAt(i).getDisplayId + ( av.getShowJVSuffix()); pg.drawString(string, 0, - (jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, - av.getCharHeight()) + av.getCharHeight()) - + ( ( (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, - startRes, startSeq, 0); + seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0); if (av.showAnnotation && (endSeq == av.alignment.getHeight())) { - pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight); - alabels.drawComponent( (Graphics2D) pg); - pg.translate(idWidth, 0); + 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); } @@ -589,17 +734,50 @@ public class AlignmentPanel 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 idWidth = calculateIdWidth().width + 4; + + 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 = totalHeight = (av.alignment.getHeight() + 2) * - ( (av.alignment.getWidth() / resWidth) + - 1) * av.charHeight; + + int totalHeight = cHeight * (maxwidth / resWidth + 1); pg.setColor(Color.white); pg.fillRect(0, 0, pwidth, pheight); @@ -613,26 +791,37 @@ public class AlignmentPanel pg.setClip(0, pi * pheight, pwidth, pheight); - int ypos = 2 * av.charHeight; + int ypos = hgap; + Font italic = new Font(av.getFont().getName(), Font.ITALIC, + av.getFont().getSize()); + pg.setFont(italic); do { for (int i = 0; i < av.alignment.getHeight(); i++) { SequenceI s = av.alignment.getSequenceAt(i); - String string = s.getName(); - - if (av.getShowFullId()) - { - string = s.getDisplayId(); - } + String string = s.getDisplayId( av.getShowJVSuffix()); pg.drawString(string, 0, - (AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos + - av.charHeight) - (av.charHeight / 5)); + ( (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.setFont(italic); + pg.translate(+3, + -ypos - + (av.getAlignment().getHeight() * av.charHeight)); } - ypos += ( (av.alignment.getHeight() + 2) * av.charHeight); + ypos += cHeight; } while (ypos < totalHeight); @@ -643,6 +832,7 @@ public class AlignmentPanel if ( (pi * pheight) < totalHeight) { return Printable.PAGE_EXISTS; + } else { @@ -650,172 +840,335 @@ public class AlignmentPanel } } - public void makeEPS() + int getVisibleIdWidth() { - int height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) * - av.chunkHeight; - int width = seqPanel.getWidth() + idPanel.getWidth(); + 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); - if (!av.getWrapAlignment()) + int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30; + int width = getVisibleIdWidth() + (maxwidth * av.charWidth); + + if (av.getWrapAlignment()) { - height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30; - width = idPanel.getWidth() + - (av.alignment.getWidth() * av.charWidth); - } + height = getWrappedHeight(); + if (System.getProperty("java.awt.headless") != null + && System.getProperty("java.awt.headless").equals("true")) + { + width = alignFrame.getWidth() - 22; + } + else + width = seqPanel.getWidth() + getVisibleIdWidth(); - if (av.getShowAnnotation()) + } + else if (av.getShowAnnotation()) { - height += annotationPanel.getPreferredSize().height; + height += annotationPanel.adjustPanelHeight() + 3; } try { - jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( - jalview.bin.Cache.getProperty( - "LAST_DIRECTORY"), new String[] - {"eps"}, - new String[] - {"Encapsulated Postscript"}, - "Encapsulated Postscript"); - chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle("Create EPS file from alignment"); - chooser.setToolTipText("Save"); - - int value = chooser.showSaveDialog(this); - - if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION) - { - return; - } - - jalview.bin.Cache.setProperty("LAST_DIRECTORY", - chooser.getSelectedFile().getParent()); - FileOutputStream out = new FileOutputStream(chooser.getSelectedFile()); - EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width, - height); + 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()) { - printWrappedAlignment(pg, width, height, 0); + if(im.getGraphics()!=null) + { + printWrappedAlignment(im.getGraphics(), width, height, 0); + im.writeImage(); + } } else { - printUnwrapped(pg, width, height, 0); + 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(); - pg.flush(); - pg.close(); } catch (Exception ex) { ex.printStackTrace(); } } - - public void makePNG() + /** + * DOCUMENT ME! + */ + public void makeEPS(File epsFile) { - int height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) * - av.chunkHeight; - int width = seqPanel.getWidth() + idPanel.getWidth(); + makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile); + } - if (!av.getWrapAlignment()) - { - height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30; - width = idPanel.getWidth() + - (av.alignment.getWidth() * av.charWidth); - } + /** + * DOCUMENT ME! + */ + public void makePNG(File pngFile) + { + makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile); + } - if (av.getShowAnnotation()) - { - height += annotationPanel.getPreferredSize().height; - } + 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(); - try + // Gen image map + ////////////////////////////////// + if (imgMapFile != null) { - jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( - jalview.bin.Cache.getProperty( - "LAST_DIRECTORY"), new String[] - {"png"}, - new String[] - {"Portable network graphics"}, - "Portable network graphics"); - chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle("Create EPS file from alignment"); - chooser.setToolTipText("Save"); - - int value = chooser.showSaveDialog(this); + 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; resres) + 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(); - if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION) + } + catch (Exception ex) { - return; + ex.printStackTrace(); } + } ///////////END OF IMAGE MAP - jalview.bin.Cache.setProperty("LAST_DIRECTORY", - chooser.getSelectedFile().getParent()); + } - FileOutputStream out = new FileOutputStream(chooser.getSelectedFile()); + int getWrappedHeight() + { + int seqPanelWidth = seqPanel.seqCanvas.getWidth(); - BufferedImage bi = new BufferedImage(width, height, - BufferedImage.TYPE_INT_RGB); - Graphics2D png = (Graphics2D) bi.getGraphics(); + //If headless, seqPanel will have 0 width + if (System.getProperty("java.awt.headless") != null + && System.getProperty("java.awt.headless").equals("true")) + { + seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth(); + } - png.setRenderingHint(RenderingHints.KEY_ANTIALIASING, - RenderingHints.VALUE_ANTIALIAS_ON); + int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth( + seqPanelWidth + ); - if (av.getWrapAlignment()) - { - printWrappedAlignment(png, width, height, 0); - } - else - { - printUnwrapped(png, width, height, 0); - } + int hgap = av.charHeight; + if (av.scaleAboveWrapped) + hgap += av.charHeight; - ImageIO.write(bi, "png", out); - out.close(); - } - catch (Exception ex) + int annotationHeight = 0; + if (av.showAnnotation) { - ex.printStackTrace(); + annotationHeight = annotationPanel.adjustPanelHeight(); } - } -} -class Preview - extends JFrame -{ - public Preview(Image image) - { - setResizable(true); - setSize(image.getWidth(this), image.getHeight(this)); - setVisible(true); - getContentPane().setLayout(new BorderLayout()); - getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER); - validate(); - repaint(); - } -} + int cHeight = av.getAlignment().getHeight() * av.charHeight + + hgap + + annotationHeight; -class PreviewPanel - extends JPanel -{ - Image image; + int maxwidth = av.alignment.getWidth(); + if (av.hasHiddenColumns) + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + + + int height = ( (maxwidth / chunkWidth) + 1) * cHeight; + + return height; + } - public PreviewPanel(Image image) + /** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ + class Preview + extends JFrame { - this.image = image; + /** + * Creates a new Preview object. + * + * @param image DOCUMENT ME! + */ + public Preview(Image image) + { + setResizable(true); + setSize(image.getWidth(this), image.getHeight(this)); + setVisible(true); + getContentPane().setLayout(new BorderLayout()); + getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER); + validate(); + repaint(); + } } - public void paintComponent(Graphics g) + /** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ + class PreviewPanel + extends JPanel { - if (image != null) + Image image; + + /** + * Creates a new PreviewPanel object. + * + * @param image DOCUMENT ME! + */ + public PreviewPanel(Image image) { - g.drawImage(image, 0, 0, this); + this.image = image; } - else + + /** + * DOCUMENT ME! + * + * @param g DOCUMENT ME! + */ + public void paintComponent(Graphics g) { - System.out.println("DEBUG:image is null"); + if (image != null) + { + g.drawImage(image, 0, 0, this); + } + else + { + System.out.println("DEBUG:image is null"); + } } } }