X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=1a48af6fbe1471e03fd96d4fbbb6dc0825674cb5;hb=588042b69abf8e60bcc950b24c283933c7dd422f;hp=7a8a811bb519747b7166daf3ed754611f662d52b;hpb=5cd8e373c75fb348ecda4d94d8a46468fb92756d;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 7a8a811..1a48af6 100755 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,46 +1,45 @@ /* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program is free software; you can redistribute it and/or -* modify it under the terms of the GNU General Public License -* as published by the Free Software Foundation; either version 2 -* of the License, or (at your option) any later version. -* -* This program is distributed in the hope that it will be useful, -* but WITHOUT ANY WARRANTY; without even the implied warranty of -* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -* GNU General Public License for more details. -* -* You should have received a copy of the GNU General Public License -* along with this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ - + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ package jalview.gui; -import jalview.jbgui.GAlignmentPanel; -import jalview.schemes.*; -import jalview.analysis.*; -import jalview.datamodel.*; +import java.io.*; +import javax.imageio.*; + import java.awt.*; import java.awt.event.*; -import java.awt.print.*; -import java.io.*; import java.awt.image.*; -import org.jibble.epsgraphics.*; -import javax.imageio.*; +import java.awt.print.*; 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 +public class AlignmentPanel + extends GAlignmentPanel implements AdjustmentListener, Printable { - - AlignViewport av; + AlignViewport av; OverviewPanel overviewPanel; - SeqPanel seqPanel; - IdPanel idPanel; + SeqPanel seqPanel; + IdPanel idPanel; IdwidthAdjuster idwidthAdjuster; public AlignFrame alignFrame; ScalePanel scalePanel; @@ -49,13 +48,15 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene // this value is set false when selection area being dragged boolean fastPaint = true; + int hextent = 0; + int vextent = 0; public AlignmentPanel(AlignFrame af, final AlignViewport av) { alignFrame = af; - this.av = av; - seqPanel = new SeqPanel (av, this); - idPanel = new IdPanel (av, this); + this.av = av; + seqPanel = new SeqPanel(av, this); + idPanel = new IdPanel(av, this); scalePanel = new ScalePanel(av, this); @@ -66,7 +67,8 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene annotationPanel = new AnnotationPanel(this); alabels = new AnnotationLabels(this); - annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize()); + annotationSpaceFillerHolder.setPreferredSize(annotationPanel. + getPreferredSize()); annotationScroller.setPreferredSize(annotationPanel.getPreferredSize()); annotationScroller.setViewportView(annotationPanel); annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER); @@ -81,27 +83,31 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene 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; - case KeyEvent.VK_UP: - alignFrame.moveSelectedSequences(true); - break; - } - } - }); + 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; + + case KeyEvent.VK_UP: + alignFrame.moveSelectedSequences(true); + + break; + } + } + }); } public void fontChanged() @@ -110,11 +116,14 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene // 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())); + scalePanelHolder.setPreferredSize(new Dimension(10, + av.charHeight + fm.getDescent())); + idSpaceFillerPanel1.setPreferredSize(new Dimension(10, + av.charHeight + fm.getDescent())); idPanel.idCanvas.gg = null; annotationPanel.adjustPanelHeight(); + Dimension d = calculateIdWidth(); d.setSize(d.width + 4, d.height); idPanel.idCanvas.setPreferredSize(d); @@ -122,11 +131,11 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene repaint(); } - Dimension calculateIdWidth() { Graphics g = this.getGraphics(); - if(g==null) + + if (g == null) { javax.swing.JFrame f = new javax.swing.JFrame(); f.addNotify(); @@ -136,70 +145,83 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene FontMetrics fm = g.getFontMetrics(av.font); AlignmentI al = av.getAlignment(); - int i = 0; - int idWidth = 0; - String id; - while (i < al.getHeight() && al.getSequenceAt(i) != null) - { - SequenceI s = al.getSequenceAt(i); - if(av.getShowFullId()) - id = s.getDisplayId(); - else - id = s.getName(); - - if (fm.stringWidth(id) > idWidth) - idWidth = fm.stringWidth(id); - i++; - } - - // Also check annotation label widths - i=0; - if(al.getAlignmentAnnotation()!=null) - { - fm = g.getFontMetrics(alabels.getFont()); - while (i < al.getAlignmentAnnotation().length) - { - String label = al.getAlignmentAnnotation()[i].label; - if (fm.stringWidth(label) > idWidth) - idWidth = fm.stringWidth(label); - i++; - } - } - - return new Dimension(idWidth, 12); - } + int i = 0; + int idWidth = 0; + String id; + while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null)) + { + SequenceI s = al.getSequenceAt(i); - public void highlightSearchResults(int [] results) - { - seqPanel.seqCanvas.highlightSearchResults( results ); + if (av.getShowFullId()) + { + id = s.getDisplayId(); + } + else + { + id = s.getName(); + } - // do we need to scroll the panel? - if(results!=null) + if (fm.stringWidth(id) > idWidth) + { + idWidth = fm.stringWidth(id); + } + + i++; + } + + // Also check annotation label widths + i = 0; + + if (al.getAlignmentAnnotation() != null) { - SequenceI seq = av.alignment.getSequenceAt(results[0]); - int start = seq.findIndex( results[1] )-1; - int end = seq.findIndex( results[2] )-1; - if( av.getStartRes() > start - || av.getEndRes() < end - || (av.getStartSeq() > results[0] - || av.getEndSeq() < results[0])) - setScrollValues(start, results[0]); + fm = g.getFontMetrics(alabels.getFont()); + + while (i < al.getAlignmentAnnotation().length) + { + String label = al.getAlignmentAnnotation()[i].label; + + if (fm.stringWidth(label) > idWidth) + { + idWidth = fm.stringWidth(label); + } + + i++; + } } - } + return new Dimension(idWidth, 12); + } + + public void highlightSearchResults(int[] results) + { + seqPanel.seqCanvas.highlightSearchResults(results); + // do we need to scroll the panel? + if (results != null) + { + SequenceI seq = av.alignment.getSequenceAt(results[0]); + int start = seq.findIndex(results[1]) - 1; + int end = seq.findIndex(results[2]) - 1; - public OverviewPanel getOverviewPanel() - { - return overviewPanel; - } + if ( (av.getStartRes() > start) || (av.getEndRes() < end) || + ( (av.getStartSeq() > results[0]) || + (av.getEndSeq() < results[0]))) + { + setScrollValues(start, results[0]); + } + } + } - public void setOverviewPanel(OverviewPanel op) - { - overviewPanel = op; - } + public OverviewPanel getOverviewPanel() + { + return overviewPanel; + } + public void setOverviewPanel(OverviewPanel op) + { + overviewPanel = op; + } public void setAnnotationVisible(boolean b) { @@ -207,7 +229,6 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene annotationScroller.setVisible(b); } - public void setWrapAlignment(boolean wrap) { scalePanelHolder.setVisible(!wrap); @@ -220,112 +241,130 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene idSpaceFillerPanel1.setVisible(!wrap); repaint(); - } - public void setColourScheme() { ColourSchemeI cs = av.getGlobalColourScheme(); - if(av.getConservationSelected()) + if (av.getConservationSelected()) { + Alignment al = (Alignment) av.getAlignment(); + Conservation c = new Conservation("All", + ResidueProperties.propHash, 3, + al.getSequences(), 0, + al.getWidth()); - 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); + c.calculate(); + c.verdict(false, av.ConsPercGaps); - av.setGlobalColourScheme( ccs ); + ConservationColourScheme ccs = new ConservationColourScheme(c, cs); + av.setGlobalColourScheme(ccs); } repaint(); } - - int hextent = 0; - int vextent = 0; - // return value is true if the scroll is valid public boolean scrollUp(boolean up) { - if(up) + if (up) { - if(vscroll.getValue()<1) + if (vscroll.getValue() < 1) + { return false; - fastPaint = false; + } + + fastPaint = false; vscroll.setValue(vscroll.getValue() - 1); } else { - if(vextent+vscroll.getValue() >= av.getAlignment().getHeight()) - return false; - fastPaint = false; + if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight()) + { + return false; + } + + fastPaint = false; vscroll.setValue(vscroll.getValue() + 1); } + fastPaint = true; + return true; } public boolean scrollRight(boolean right) { - if (right) { if (hscroll.getValue() < 1) + { return false; + } + fastPaint = false; hscroll.setValue(hscroll.getValue() - 1); } else { - if (hextent + hscroll.getValue() >= av.getAlignment().getWidth()) + if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth()) + { return false; + } + fastPaint = false; hscroll.setValue(hscroll.getValue() + 1); } + fastPaint = true; + return true; } - public void setScrollValues(int x, int y) { - av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1); + av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - + 1); - hextent = seqPanel.seqCanvas.getWidth()/av.charWidth; - vextent = seqPanel.seqCanvas.getHeight()/av.charHeight; + hextent = seqPanel.seqCanvas.getWidth() / av.charWidth; + vextent = seqPanel.seqCanvas.getHeight() / av.charHeight; - if(hextent > av.alignment.getWidth()) + if (hextent > av.alignment.getWidth()) + { hextent = av.alignment.getWidth(); - if(vextent > av.alignment.getHeight()) + } + + if (vextent > av.alignment.getHeight()) + { vextent = av.alignment.getHeight(); + } - if(hextent+x > av.getAlignment().getWidth()) - x = av.getAlignment().getWidth()- hextent; + if ( (hextent + x) > av.getAlignment().getWidth()) + { + x = av.getAlignment().getWidth() - hextent; + } - if(vextent+y > av.getAlignment().getHeight()) + if ( (vextent + y) > av.getAlignment().getHeight()) + { y = av.getAlignment().getHeight() - vextent; + } - if(y<0) + if (y < 0) + { y = 0; + } - if(x<0) - x=0; - - hscroll.setValues(x,hextent,0,av.getAlignment().getWidth()); - vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() ); - - + if (x < 0) + { + x = 0; + } + hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth()); + vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight()); } - public void adjustmentValueChanged(AdjustmentEvent evt) { int oldX = av.getStartRes(); @@ -335,30 +374,38 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene { int x = hscroll.getValue(); av.setStartRes(x); - av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1); + av.setEndRes( (x + + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1); } if (evt.getSource() == vscroll) { int offy = vscroll.getValue(); + if (av.getWrapAlignment()) { - int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()); - av.setStartRes( vscroll.getValue() * rowSize ); - av.setEndRes( (vscroll.getValue()+1) * rowSize ); + int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel. + seqCanvas.getWidth()); + av.setStartRes(vscroll.getValue() * rowSize); + av.setEndRes( (vscroll.getValue() + 1) * rowSize); } else { av.setStartSeq(offy); - av.setEndSeq(offy + seqPanel.seqCanvas.getHeight() / av.getCharHeight()); + av.setEndSeq(offy + + (seqPanel.seqCanvas.getHeight() / av.getCharHeight())); } } - if(overviewPanel!=null) + if (overviewPanel != null) + { overviewPanel.setBoxPosition(); + } - if(av.getWrapAlignment() || !fastPaint) + if (av.getWrapAlignment() || !fastPaint) + { repaint(); + } else { idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY); @@ -366,16 +413,18 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene av.getStartSeq() - oldY); scalePanel.repaint(); + if (av.getShowAnnotation()) + { annotationPanel.fastPaint(av.getStartRes() - oldX); + } } - } - public void paintComponent(Graphics g) { invalidate(); + Dimension d = idPanel.idCanvas.getPreferredSize(); idPanelHolder.setPreferredSize(d); hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12)); @@ -383,7 +432,8 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene if (av.getWrapAlignment()) { - int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()); + int max = av.alignment.getWidth() / + seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()); vscroll.setMaximum(max); vscroll.setUnitIncrement(1); vscroll.setVisibleAmount(1); @@ -392,226 +442,270 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene { setScrollValues(av.getStartRes(), av.getStartSeq()); } - - - } - public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException + public int print(Graphics pg, PageFormat pf, int pi) + throws PrinterException { - pg.translate((int)pf.getImageableX(), (int)pf.getImageableY()); + 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); + { + return printWrappedAlignment(pg, pwidth, pheight, pi); + } else - return printUnwrapped(pg,pwidth, pheight,pi); + { + return printUnwrapped(pg, pwidth, pheight, pi); + } } - public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException + public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) + throws PrinterException { + int idWidth = calculateIdWidth().width + 4; + FontMetrics fm = getFontMetrics(av.getFont()); + int scaleHeight = av.charHeight + fm.getDescent(); - int idWidth = calculateIdWidth().width + 4; - FontMetrics fm = getFontMetrics(av.getFont()); - int scaleHeight = av.charHeight + fm.getDescent(); + pg.setColor(Color.white); + pg.fillRect(0, 0, pwidth, pheight); + pg.setFont(av.getFont()); - 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(); - //////////////////////////////////// - /// 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 totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) - 1; + int pagesWide = (av.getAlignment().getWidth() / totalRes) + 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 startRes, endRes, startSeq, endSeq; - startRes = (pi % pagesWide) * totalRes; - endRes = startRes + totalRes - 1; - if (endRes > av.getAlignment().getWidth()-1) - endRes = av.getAlignment().getWidth()-1; + ///////////////////////////// + /// Only print these sequences and residues on this page + int endRes; - startSeq = (pi / pagesWide) * totalSeq; - endSeq = startSeq + totalSeq; - if (endSeq > av.getAlignment().getHeight()) - endSeq = av.getAlignment().getHeight(); + ///////////////////////////// + /// Only print these sequences and residues on this page + int startSeq; - int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight; + ///////////////////////////// + /// Only print these sequences and residues on this page + int endSeq; + startRes = (pi % pagesWide) * totalRes; + endRes = (startRes + totalRes) - 1; - if (av.showAnnotation) - pagesHigh += annotationPanel.getHeight(); + if (endRes > (av.getAlignment().getWidth() - 1)) + { + endRes = av.getAlignment().getWidth() - 1; + } + + startSeq = (pi / pagesWide) * totalSeq; + endSeq = startSeq + totalSeq; - pagesHigh /= pheight; + if (endSeq > av.getAlignment().getHeight()) + { + endSeq = av.getAlignment().getHeight(); + } - if (pi >= pagesWide * pagesHigh) - return Printable.NO_SUCH_PAGE; + int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight; - //draw Scale - pg.translate(idWidth, 0); - scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight); - pg.translate( -idWidth, scaleHeight); - //////////////// - // Draw the ids - Color currentColor = null; - Color currentTextColor = null; - for (int i = startSeq; i < endSeq; i++) - { - if (av.getSelectionGroup() != null && - av.getSelectionGroup().sequences. - contains(av.getAlignment().getSequenceAt(i))) - { - currentColor = Color.gray; - currentTextColor = Color.black; - } - else - { - currentColor = av.getAlignment().getSequenceAt(i).getColor(); - currentTextColor = Color.black; - } + if (av.showAnnotation) + { + pagesHigh += annotationPanel.getHeight(); + } - pg.setColor(currentColor); - pg.fillRect(0, - jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, - av.getCharHeight()), - idWidth, - av.getCharHeight()); + pagesHigh /= pheight; + + if (pi >= (pagesWide * pagesHigh)) + { + return Printable.NO_SUCH_PAGE; + } - pg.setColor(currentTextColor); + //draw Scale + pg.translate(idWidth, 0); + scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight); + pg.translate( -idWidth, scaleHeight); - String string = av.getAlignment().getSequenceAt(i).getName(); - if (av.getShowFullId()) - string = av.getAlignment().getSequenceAt(i).getDisplayId(); + //////////////// + // Draw the ids + Color currentColor = null; + Color currentTextColor = null; - pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight - (startSeq, i, av.getCharHeight()) + av.getCharHeight() - - (av.getCharHeight() / 5)); + for (int i = startSeq; i < endSeq; i++) + { + if ( (av.getSelectionGroup() != null) && + av.getSelectionGroup().sequences.contains( + av.getAlignment().getSequenceAt(i))) + { + currentColor = Color.gray; + currentTextColor = Color.black; + } + else + { + currentColor = av.getAlignment().getSequenceAt(i).getColor(); + currentTextColor = Color.black; } - // draw main sequence panel - pg.translate(idWidth, 0); - seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, - startRes, startSeq, 0); + pg.setColor(currentColor); + pg.fillRect(0, + jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, + av.getCharHeight()), idWidth, av.getCharHeight()); + pg.setColor(currentTextColor); - if (av.showAnnotation && endSeq == av.alignment.getHeight()) + String string = av.getAlignment().getSequenceAt(i).getName(); + + if (av.getShowFullId()) { - pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight); - alabels.drawComponent( (Graphics2D) pg); - pg.translate(idWidth, 0); - annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes+1); + string = av.getAlignment().getSequenceAt(i).getDisplayId(); } - return Printable.PAGE_EXISTS; + pg.drawString(string, 0, + (jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, + av.getCharHeight()) + av.getCharHeight()) - + (av.getCharHeight() / 5)); + } - } + // draw main sequence panel + pg.translate(idWidth, 0); + seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, + startRes, startSeq, 0); + if (av.showAnnotation && (endSeq == av.alignment.getHeight())) + { + pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight); + alabels.drawComponent( (Graphics2D) pg); + pg.translate(idWidth, 0); + annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes + + 1); + } - public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException + return Printable.PAGE_EXISTS; + } + + public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, + int pi) + throws PrinterException { - int idWidth = calculateIdWidth().width + 4; + int idWidth = calculateIdWidth().width + 4; - int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth - idWidth); - int totalHeight = totalHeight = (av.alignment.getHeight() + 2) * - ( (av.alignment.getWidth() - / resWidth) + 1) * av.charHeight; + int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth - + idWidth); + int totalHeight = totalHeight = (av.alignment.getHeight() + 2) * + ( (av.alignment.getWidth() / resWidth) + + 1) * av.charHeight; + pg.setColor(Color.white); + pg.fillRect(0, 0, pwidth, pheight); + pg.setFont(av.getFont()); - pg.setColor(Color.white); - pg.fillRect(0, 0, pwidth, pheight); - pg.setFont(av.getFont()); + //////////////// + // Draw the ids + pg.setColor(Color.black); - //////////////// - // Draw the ids - pg.setColor(Color.black); + pg.translate(0, -pi * pheight); - pg.translate(0, -pi * pheight); + pg.setClip(0, pi * pheight, pwidth, pheight); - pg.setClip(0,pi*pheight,pwidth, pheight); + int ypos = 2 * av.charHeight; - int ypos = 2 * av.charHeight; - do + do + { + for (int i = 0; i < av.alignment.getHeight(); i++) { - for (int i = 0; i < av.alignment.getHeight(); i++) - { - SequenceI s = av.alignment.getSequenceAt(i); - String string = s.getName(); - if (av.getShowFullId()) - string = s.getDisplayId(); - - pg.drawString(string, 0, - AlignmentUtil.getPixelHeight(0, i, av.charHeight) + - ypos + - av.charHeight - (av.charHeight / 5)); + SequenceI s = av.alignment.getSequenceAt(i); + String string = s.getName(); + if (av.getShowFullId()) + { + string = s.getDisplayId(); } - ypos += (av.alignment.getHeight() + 2) * av.charHeight; - + pg.drawString(string, 0, + (AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos + + av.charHeight) - (av.charHeight / 5)); } - 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; + ypos += ( (av.alignment.getHeight() + 2) * av.charHeight); + } + while (ypos < totalHeight); + pg.translate(idWidth, 0); + seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0); + if ( (pi * pheight) < totalHeight) + { + return Printable.PAGE_EXISTS; + } + else + { + return Printable.NO_SUCH_PAGE; + } } - public void makeEPS() { - int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight; + int height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) * + av.chunkHeight; int width = seqPanel.getWidth() + idPanel.getWidth(); if (!av.getWrapAlignment()) { - height = (av.alignment.getHeight()+1) * av.charHeight + 30; - width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth; + height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30; + width = idPanel.getWidth() + + (av.alignment.getWidth() * av.charWidth); + } + + if (av.getShowAnnotation()) + { + height += annotationPanel.getPreferredSize().height; } - if(av.getShowAnnotation()) - { - height += annotationPanel.getPreferredSize().height; - } try { - jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty( - "LAST_DIRECTORY"), - new String[]{"eps"}, - new String[]{"Encapsulated Postscript"}, - "Encapsulated Postscript"); + 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.bin.Cache.setProperty("LAST_DIRECTORY", + chooser.getSelectedFile().getParent()); - if (av.getWrapAlignment()) - printWrappedAlignment(pg, width, height, 0); - else - printUnwrapped(pg, width, height, 0); + FileOutputStream out = new FileOutputStream(chooser.getSelectedFile()); + EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width, + height); + if (av.getWrapAlignment()) + { + printWrappedAlignment(pg, width, height, 0); + } + else + { + printUnwrapped(pg, width, height, 0); + } - pg.flush(); - pg.close(); + pg.flush(); + pg.close(); } catch (Exception ex) { @@ -621,64 +715,76 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene public void makePNG() { - int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight; - int width = seqPanel.getWidth() + idPanel.getWidth(); - - if (!av.getWrapAlignment()) - { - height = (av.alignment.getHeight()+1) * av.charHeight + 30; - width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth; - } - - if(av.getShowAnnotation()) - { - height += annotationPanel.getPreferredSize().height; - } + int height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) * + av.chunkHeight; + int width = seqPanel.getWidth() + idPanel.getWidth(); + if (!av.getWrapAlignment()) + { + height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30; + width = idPanel.getWidth() + + (av.alignment.getWidth() * av.charWidth); + } + if (av.getShowAnnotation()) + { + height += annotationPanel.getPreferredSize().height; + } try { - 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"); + jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( + jalview.bin.Cache.getProperty( + "LAST_DIRECTORY"), new String[] + {"png"}, + new String[] + {"Portable network graphics"}, + "Portable network graphics"); chooser.setFileView(new jalview.io.JalviewFileView()); chooser.setDialogTitle("Create EPS file from alignment"); chooser.setToolTipText("Save"); int value = chooser.showSaveDialog(this); + if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION) + { return; + } + + jalview.bin.Cache.setProperty("LAST_DIRECTORY", + chooser.getSelectedFile().getParent()); - jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent()); FileOutputStream out = new FileOutputStream(chooser.getSelectedFile()); - BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB); - Graphics2D png = (Graphics2D)bi.getGraphics(); + BufferedImage bi = new BufferedImage(width, height, + BufferedImage.TYPE_INT_RGB); + Graphics2D png = (Graphics2D) bi.getGraphics(); - png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON); + png.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); - if (av.getWrapAlignment()) - printWrappedAlignment(png, width, height, 0); - else - printUnwrapped(png, width, height, 0); + if (av.getWrapAlignment()) + { + printWrappedAlignment(png, width, height, 0); + } + else + { + printUnwrapped(png, width, height, 0); + } - ImageIO.write(bi, "png", out); - out.close(); + ImageIO.write(bi, "png", out); + out.close(); } catch (Exception ex) { ex.printStackTrace(); } } - } -class Preview extends JFrame +class Preview + extends JFrame { - public Preview(Image image) { setResizable(true); @@ -691,22 +797,25 @@ class Preview extends JFrame } } -class PreviewPanel extends JPanel +class PreviewPanel + extends JPanel { Image image; + public PreviewPanel(Image image) { this.image = image; } + public void paintComponent(Graphics g) { - if(image!=null) - g.drawImage(image,0,0,this); + if (image != null) + { + g.drawImage(image, 0, 0, this); + } else + { System.out.println("DEBUG:image is null"); + } } } - - - -