X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=9278bc1dac40992d772d9377f7b8308f625c908f;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=989575348842fdc3b9046382b7998935ea6b1621;hpb=e5127e5f27f02c8f328539eaac68eabfbee1d135;p=jalview.git
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 9895753..9278bc1 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,693 +1,1392 @@
-package jalview.gui;
-
-import jalview.jbgui.GAlignmentPanel;
-import jalview.schemes.*;
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.print.*;
-import java.io.*;
-import java.awt.image.*;
-import org.jibble.epsgraphics.*;
-import javax.imageio.*;
-import javax.swing.*;
-
-
-
-public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable
-{
-
- AlignViewport av;
- OverviewPanel overviewPanel;
- SeqPanel seqPanel;
- IdPanel idPanel;
- IdwidthAdjuster idwidthAdjuster;
- public AlignFrame alignFrame;
- ScalePanel scalePanel;
- AnnotationPanel annotationPanel;
- AnnotationLabels alabels;
-
- // this value is set false when selection area being dragged
- boolean fastPaint = true;
-
- public AlignmentPanel(AlignFrame af, final AlignViewport av)
- {
- alignFrame = af;
- this.av = av;
- seqPanel = new SeqPanel (av, this);
- idPanel = new IdPanel (av, this);
-
- scalePanel = new ScalePanel(av, this);
-
- idPanelHolder.add(idPanel, BorderLayout.CENTER);
- idwidthAdjuster = new IdwidthAdjuster(this);
- idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
-
- annotationPanel = new AnnotationPanel(this);
- alabels = new AnnotationLabels(this);
-
- annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());
- annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
- annotationScroller.setViewportView(annotationPanel);
- annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
-
- fontChanged();
-
- scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
- seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
-
- setScrollValues(0, 0);
-
- 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;
- }
- }
- });
- }
-
- 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;
- annotationPanel.adjustPanelHeight();
- Dimension d = calculateIdWidth();
- d.setSize(d.width + 4, d.height);
- idPanel.idCanvas.setPreferredSize(d);
- hscrollFillerPanel.setPreferredSize(d);
- repaint();
- }
-
-
- Dimension calculateIdWidth()
- {
- Graphics g = this.getGraphics();
- if(g==null)
- {
- javax.swing.JFrame f = new javax.swing.JFrame();
- f.addNotify();
- g = f.getGraphics();
- }
-
- FontMetrics fm = g.getFontMetrics(av.font);
- AlignmentI al = av.getAlignment();
-
- int i = 0;
- int idWidth = 0;
- String id;
- while (i < al.getHeight() && al.getSequenceAt(i) != null)
- {
- SequenceI s = al.getSequenceAt(i);
- if(av.getShowFullId())
- id = s.getDisplayId();
- else
- id = s.getName();
-
- if (fm.stringWidth(id) > idWidth)
- idWidth = fm.stringWidth(id);
- i++;
- }
-
- // Also check annotation label widths
- i=0;
- if(al.getAlignmentAnnotation()!=null)
- {
- fm = g.getFontMetrics(alabels.getFont());
- while (i < al.getAlignmentAnnotation().length)
- {
- String label = al.getAlignmentAnnotation()[i].label;
- if (fm.stringWidth(label) > idWidth)
- idWidth = fm.stringWidth(label);
- i++;
- }
- }
-
- return new Dimension(idWidth, 12);
- }
-
-
- public void highlightSearchResults(int [] results)
- {
- seqPanel.seqCanvas.highlightSearchResults( results );
-
- // do we need to scroll the panel?
- if(results!=null)
- {
- 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]);
- }
-
- }
-
-
- public OverviewPanel getOverviewPanel()
- {
- return overviewPanel;
- }
-
- public void setOverviewPanel(OverviewPanel op)
- {
- overviewPanel = op;
- }
-
-
- public void setAnnotationVisible(boolean b)
- {
- annotationSpaceFillerHolder.setVisible(b);
- annotationScroller.setVisible(b);
- }
-
-
- public void setWrapAlignment(boolean wrap)
- {
- scalePanelHolder.setVisible(!wrap);
- hscroll.setVisible(!wrap);
- idwidthAdjuster.setVisible(!wrap);
-
- av.setShowAnnotation(!wrap);
- annotationScroller.setVisible(!wrap);
- annotationSpaceFillerHolder.setVisible(!wrap);
- idSpaceFillerPanel1.setVisible(!wrap);
-
- repaint();
-
- }
-
-
- public void setColourScheme()
- {
- ColourSchemeI cs = av.getGlobalColourScheme();
-
- if(av.getConservationSelected())
- {
-
- 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 );
-
- }
-
- repaint();
- }
-
-
- int hextent = 0;
- int vextent = 0;
-
- // 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;
- }
-
- public boolean scrollRight(boolean right)
- {
-
- if (right)
- {
- if (hscroll.getValue() < 1)
- return false;
- fastPaint = false;
- hscroll.setValue(hscroll.getValue() - 1);
- }
- else
- {
- if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
- return false;
- fastPaint = false;
- hscroll.setValue(hscroll.getValue() + 1);
- }
- fastPaint = true;
- return true;
- }
-
-
- public void setScrollValues(int x, int y)
- {
- av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
-
- hextent = seqPanel.seqCanvas.getWidth()/av.charWidth;
- vextent = seqPanel.seqCanvas.getHeight()/av.charHeight;
-
- if(hextent > av.alignment.getWidth())
- hextent = av.alignment.getWidth();
- if(vextent > av.alignment.getHeight())
- vextent = av.alignment.getHeight();
-
- if(hextent+x > av.getAlignment().getWidth())
- x = av.getAlignment().getWidth()- hextent;
-
- if(vextent+y > av.getAlignment().getHeight())
- y = av.getAlignment().getHeight() - vextent;
-
- if(y<0)
- y = 0;
-
- if(x<0)
- x=0;
-
- hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
- vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
-
-
-
- }
-
-
- public void adjustmentValueChanged(AdjustmentEvent evt)
- {
- int oldX = av.getStartRes();
- int oldY = av.getStartSeq();
-
- if (evt.getSource() == hscroll)
- {
- int x = hscroll.getValue();
- av.setStartRes(x);
- av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
- }
-
- if (evt.getSource() == vscroll)
- {
- int offy = vscroll.getValue();
- if (av.getWrapAlignment())
- {
- int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
- av.setStartRes( vscroll.getValue() * rowSize );
- av.setEndRes( (vscroll.getValue()+1) * rowSize );
- }
- else
- {
- av.setStartSeq(offy);
- av.setEndSeq(offy + seqPanel.seqCanvas.getHeight() / av.getCharHeight());
- }
- }
-
- if(overviewPanel!=null)
- overviewPanel.setBoxPosition();
-
- if(av.getWrapAlignment() || !fastPaint)
- repaint();
- else
- {
- idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
- seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
- 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));
- validate();
-
- if (av.getWrapAlignment())
- {
- int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
- vscroll.setMaximum(max);
- vscroll.setUnitIncrement(1);
- vscroll.setVisibleAmount(1);
- }
- else
- {
- setScrollValues(av.getStartRes(), av.getStartSeq());
- }
-
-
-
- }
-
- public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
- {
- pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
-
- int pwidth = (int) pf.getImageableWidth();
- int pheight = (int) pf.getImageableHeight();
-
- if (av.getWrapAlignment())
- return printWrappedAlignment(pg, pwidth,pheight, pi);
- else
- return printUnwrapped(pg,pwidth, pheight,pi);
- }
-
- public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
- {
-
- int idWidth = calculateIdWidth().width + 4;
- 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, endRes, startSeq, 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.getHeight();
-
- 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;
- for (int i = startSeq; i < endSeq; i++)
- {
- if (av.getSelectionGroup() != null &&
- av.getSelectionGroup().sequences.
- contains(av.getAlignment().getSequenceAt(i)))
- {
- currentColor = Color.gray;
- currentTextColor = Color.black;
- }
- else
- {
- currentColor = av.getAlignment().getSequenceAt(i).getColor();
- currentTextColor = Color.black;
- }
-
- pg.setColor(currentColor);
- pg.fillRect(0,
- jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,
- av.getCharHeight()),
- idWidth,
- av.getCharHeight());
-
- pg.setColor(currentTextColor);
-
- String string = av.getAlignment().getSequenceAt(i).getName();
- if (av.getShowFullId())
- string = av.getAlignment().getSequenceAt(i).getDisplayId();
-
- pg.drawString(string, 0, 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);
- }
-
- return Printable.PAGE_EXISTS;
-
- }
-
-
- public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
- {
- int idWidth = calculateIdWidth().width + 4;
-
- int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth - idWidth);
- int totalHeight = totalHeight = (av.alignment.getHeight() + 2) *
- ( (av.alignment.getWidth()
- / resWidth) + 1) * av.charHeight;
-
-
- pg.setColor(Color.white);
- pg.fillRect(0, 0, pwidth, pheight);
- pg.setFont(av.getFont());
-
- ////////////////
- // Draw the ids
- pg.setColor(Color.black);
-
- pg.translate(0, -pi * pheight);
-
- pg.setClip(0,pi*pheight,pwidth, pheight);
-
- int ypos = 2 * av.charHeight;
- do
- {
- for (int i = 0; i < av.alignment.getHeight(); i++)
- {
- SequenceI s = av.alignment.getSequenceAt(i);
- String string = s.getName();
- if (av.getShowFullId())
- string = s.getDisplayId();
-
- pg.drawString(string, 0,
- AlignmentUtil.getPixelHeight(0, i, av.charHeight) +
- ypos +
- av.charHeight - (av.charHeight / 5));
-
- }
-
- ypos += (av.alignment.getHeight() + 2) * av.charHeight;
-
- }
- while (ypos < totalHeight);
-
- pg.translate(idWidth, 0);
-
- seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
-
- if (pi * pheight < totalHeight)
- return Printable.PAGE_EXISTS;
- else
- return Printable.NO_SUCH_PAGE;
-
-
-
- }
-
-
- public void makeEPS()
- {
- 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[]{"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);
-
- if (av.getWrapAlignment())
- printWrappedAlignment(pg, width, height, 0);
- else
- printUnwrapped(pg, width, height, 0);
-
-
- pg.flush();
- pg.close();
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- public void 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;
- }
-
-
-
- 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");
- 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());
-
- BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
- Graphics2D png = (Graphics2D)bi.getGraphics();
-
- png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);
-
- if (av.getWrapAlignment())
- printWrappedAlignment(png, width, height, 0);
- else
- printUnwrapped(png, width, height, 0);
-
- ImageIO.write(bi, "png", out);
- out.close();
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
-}
-
-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();
- }
-}
-
-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);
- else
- System.out.println("DEBUG:image is null");
- }
-}
-
-
-
-
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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 .
+ */
+package jalview.gui;
+
+import java.beans.*;
+import java.io.*;
+import java.util.Hashtable;
+import java.util.Vector;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.print.*;
+import javax.swing.*;
+
+import jalview.bin.Cache;
+import jalview.datamodel.*;
+import jalview.jbgui.*;
+import jalview.schemes.*;
+import jalview.structure.SelectionSource;
+
+/**
+ * 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();
+ }
+
+ /**
+ * 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()
+ {
+ Container c = new Container();
+
+ FontMetrics fm = c.getFontMetrics(new Font(av.font.getName(),
+ Font.ITALIC, av.font.getSize()));
+
+ AlignmentI al = av.getAlignment();
+ int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
+ int maxwidth = Math.max(20, Math.min(afwidth - 200, (int) 2 * afwidth
+ / 3));
+ 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(Math.min(maxwidth, idWidth), 12);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param results
+ * DOCUMENT ME!
+ */
+ public void highlightSearchResults(SearchResults results)
+ {
+ scrollToPosition(results);
+ seqPanel.seqCanvas.highlightSearchResults(results);
+ }
+
+ /**
+ * scroll the view to show the position of the highlighted region in results
+ * (if any) and redraw the overview
+ *
+ * @param results
+ */
+ public boolean scrollToPosition(SearchResults results)
+ {
+ return scrollToPosition(results, true);
+ }
+
+ /**
+ * scroll the view to show the position of the highlighted region in results
+ * (if any)
+ *
+ * @param results
+ * @param redrawOverview
+ * - when set, the overview will be recalculated (takes longer)
+ * @return false if results were not found
+ */
+ public boolean scrollToPosition(SearchResults results,
+ boolean redrawOverview)
+ {
+ int startv, endv, starts, ends, width;
+ // 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 nullpointereexceptions raised here.
+ if (results != null && results.getSize() > 0 && av != null
+ && av.alignment != null)
+ {
+ int seqIndex = av.alignment.findIndex(results);
+ if (seqIndex == -1)
+ {
+ return false;
+ }
+ SequenceI seq = av.alignment.getSequenceAt(seqIndex);
+
+ int[] r = results.getResults(seq, 0, av.alignment.getWidth()); // results.getResults(seq,
+ // seq.getStart(),
+ // seq.getEnd());
+ // TODO: VAMSAS: fix hidden column issue where scroll to left from C
+ // terminus is not visible
+ if (r == null)
+ {
+ return false;
+ }
+ int start = r[0];
+ int end = r[1];
+ // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); // DEBUG
+ if (start < 0)
+ {
+ return false;
+ }
+ if (end == seq.getEnd())
+ {
+ return false;
+ }
+ if (!av.wrapAlignment)
+ {
+ if ((startv = av.getStartRes()) >= start)
+ {
+ setScrollValues(start - 1, seqIndex);
+ }
+ else if ((endv = av.getEndRes()) <= end)
+ {
+ setScrollValues(startv + 1 + end - endv, seqIndex);
+ }
+ else if ((starts = av.getStartSeq()) > seqIndex)
+ {
+ setScrollValues(av.getStartRes(), seqIndex);
+ }
+ else if ((ends = av.getEndSeq()) <= seqIndex)
+ {
+ setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
+ }
+ }
+ else
+ {
+ scrollToWrappedVisible(start);
+ }
+ }
+ if (!redrawOverview && overviewPanel != null)
+ {
+ overviewPanel.setBoxPosition();
+ }
+ paintAlignment(!redrawOverview);
+ return 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()
+ {
+ // TODO: display vertical annotation scrollbar if necessary
+ // this is called after loading new annotation onto alignment
+ if (alignFrame.getHeight() == 0)
+ {
+ System.out.println("NEEDS FIXING");
+ }
+
+ int height = annotationPanel.adjustPanelHeight();
+
+ if (hscroll.isVisible())
+ {
+ height += hscroll.getPreferredSize().height;
+ }
+ if (height > alignFrame.getHeight() / 2)
+ {
+ height = alignFrame.getHeight() / 2;
+ }
+
+ hscroll.addNotify();
+
+ annotationScroller.setPreferredSize(new Dimension(annotationScroller
+ .getWidth(), height));
+
+ annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+ annotationSpaceFillerHolder.getWidth(), height));
+ annotationScroller.validate();// repaint();
+ addNotify();
+ 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)
+ {
+ // System.err.println("Scroll to "+x+","+y);
+ if (av == null || av.alignment == null)
+ {
+ return;
+ }
+ int width = av.alignment.getWidth();
+ int height = av.alignment.getHeight();
+
+ if (av.hasHiddenColumns)
+ {
+ width = av.getColumnSelection().findColumnPosition(width);
+ }
+
+ av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) - 1);
+
+ hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
+ vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
+
+ if (hextent > width)
+ {
+ hextent = width;
+ }
+
+ if (vextent > height)
+ {
+ vextent = height;
+ }
+
+ if ((hextent + x) > width)
+ {
+ x = width - hextent;
+ }
+
+ if ((vextent + y) > height)
+ {
+ y = height - vextent;
+ }
+
+ if (y < 0)
+ {
+ y = 0;
+ }
+
+ if (x < 0)
+ {
+ x = 0;
+ }
+
+ hscroll.setValues(x, hextent, 0, width);
+ vscroll.setValues(y, vextent, 0, height);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void adjustmentValueChanged(AdjustmentEvent evt)
+ {
+
+ int oldX = av.getStartRes();
+ int oldY = av.getStartSeq();
+
+ if (evt.getSource() == hscroll)
+ {
+ int x = hscroll.getValue();
+ av.setStartRes(x);
+ av
+ .setEndRes((x + (seqPanel.seqCanvas.getWidth() / av
+ .getCharWidth())) - 1);
+ }
+
+ if (evt.getSource() == vscroll)
+ {
+ int offy = vscroll.getValue();
+
+ if (av.getWrapAlignment())
+ {
+ if (offy > -1)
+ {
+ int rowSize = seqPanel.seqCanvas
+ .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+ av.setStartRes(offy * rowSize);
+ av.setEndRes((offy + 1) * rowSize);
+ }
+ else
+ {
+ // This is only called if file loaded is a jar file that
+ // was wrapped when saved and user has wrap alignment true
+ // as preference setting
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ setScrollValues(av.getStartRes(), av.getStartSeq());
+ }
+ });
+ }
+ }
+ else
+ {
+ av.setStartSeq(offy);
+ av.setEndSeq(offy
+ + (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
+ }
+ }
+
+ if (overviewPanel != null)
+ {
+ overviewPanel.setBoxPosition();
+ }
+
+ int scrollX = av.startRes - oldX;
+ int scrollY = av.startSeq - oldY;
+
+ if (av.getWrapAlignment() || !fastPaint)
+ {
+ repaint();
+ }
+ else
+ {
+ // Make sure we're not trying to draw a panel
+ // larger than the visible window
+ if (scrollX > av.endRes - av.startRes)
+ {
+ scrollX = av.endRes - av.startRes;
+ }
+ else if (scrollX < av.startRes - av.endRes)
+ {
+ scrollX = av.startRes - av.endRes;
+ }
+
+ if (scrollX != 0 || scrollY != 0)
+ {
+ idPanel.idCanvas.fastPaint(scrollY);
+ seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
+ scalePanel.repaint();
+
+ if (av.getShowAnnotation())
+ {
+ annotationPanel.fastPaint(scrollX);
+ }
+ }
+ }
+ }
+
+ public void paintAlignment(boolean updateOverview)
+ {
+ repaint();
+
+ if (updateOverview)
+ {
+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager().sequenceColoursChanged(this);
+
+ if (overviewPanel != null)
+ {
+ overviewPanel.updateOverviewImage();
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ */
+ public void paintComponent(Graphics g)
+ {
+ invalidate();
+
+ Dimension d = idPanel.idCanvas.getPreferredSize();
+ idPanelHolder.setPreferredSize(d);
+ hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
+ validate();
+
+ if (av.getWrapAlignment())
+ {
+ int maxwidth = av.alignment.getWidth();
+
+ if (av.hasHiddenColumns)
+ {
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ }
+
+ int canvasWidth = seqPanel.seqCanvas
+ .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+ if (canvasWidth > 0)
+ {
+ int max = maxwidth
+ / seqPanel.seqCanvas
+ .getWrappedCanvasWidth(seqPanel.seqCanvas
+ .getWidth()) + 1;
+ vscroll.setMaximum(max);
+ vscroll.setUnitIncrement(1);
+ vscroll.setVisibleAmount(1);
+ }
+ }
+ else
+ {
+ setScrollValues(av.getStartRes(), av.getStartSeq());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pg
+ * DOCUMENT ME!
+ * @param pf
+ * DOCUMENT ME!
+ * @param pi
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws PrinterException
+ * DOCUMENT ME!
+ */
+ public int print(Graphics pg, PageFormat pf, int pi)
+ throws PrinterException
+ {
+ pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
+
+ int pwidth = (int) pf.getImageableWidth();
+ int pheight = (int) pf.getImageableHeight();
+
+ if (av.getWrapAlignment())
+ {
+ return printWrappedAlignment(pg, pwidth, pheight, pi);
+ }
+ else
+ {
+ return printUnwrapped(pg, pwidth, pheight, pi);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pg
+ * DOCUMENT ME!
+ * @param pwidth
+ * DOCUMENT ME!
+ * @param pheight
+ * DOCUMENT ME!
+ * @param pi
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws PrinterException
+ * DOCUMENT ME!
+ */
+ public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
+ throws PrinterException
+ {
+ int idWidth = getVisibleIdWidth();
+ FontMetrics fm = getFontMetrics(av.getFont());
+ int scaleHeight = av.charHeight + fm.getDescent();
+
+ pg.setColor(Color.white);
+ pg.fillRect(0, 0, pwidth, pheight);
+ pg.setFont(av.getFont());
+
+ // //////////////////////////////////
+ // / How many sequences and residues can we fit on a printable page?
+ int totalRes = (pwidth - idWidth) / av.getCharWidth();
+
+ int totalSeq = (int) ((pheight - scaleHeight) / av.getCharHeight()) - 1;
+
+ int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
+
+ // ///////////////////////////
+ // / Only print these sequences and residues on this page
+ int startRes;
+
+ // ///////////////////////////
+ // / Only print these sequences and residues on this page
+ int endRes;
+
+ // ///////////////////////////
+ // / Only print these sequences and residues on this page
+ int startSeq;
+
+ // ///////////////////////////
+ // / Only print these sequences and residues on this page
+ int endSeq;
+ startRes = (pi % pagesWide) * totalRes;
+ endRes = (startRes + totalRes) - 1;
+
+ if (endRes > (av.getAlignment().getWidth() - 1))
+ {
+ endRes = av.getAlignment().getWidth() - 1;
+ }
+
+ startSeq = (pi / pagesWide) * totalSeq;
+ endSeq = startSeq + totalSeq;
+
+ if (endSeq > av.getAlignment().getHeight())
+ {
+ endSeq = av.getAlignment().getHeight();
+ }
+
+ int pagesHigh = ((av.alignment.getHeight() / totalSeq) + 1) * pheight;
+
+ if (av.showAnnotation)
+ {
+ pagesHigh += annotationPanel.adjustPanelHeight() + 3;
+ }
+
+ pagesHigh /= pheight;
+
+ if (pi >= (pagesWide * pagesHigh))
+ {
+ return Printable.NO_SUCH_PAGE;
+ }
+
+ // draw Scale
+ pg.translate(idWidth, 0);
+ scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth,
+ scaleHeight);
+ pg.translate(-idWidth, scaleHeight);
+
+ // //////////////
+ // Draw the ids
+ Color currentColor = null;
+ Color currentTextColor = null;
+
+ pg.setFont(idPanel.idCanvas.idfont);
+
+ SequenceI seq;
+ for (int i = startSeq; i < endSeq; i++)
+ {
+ seq = av.getAlignment().getSequenceAt(i);
+ if ((av.getSelectionGroup() != null)
+ && av.getSelectionGroup().getSequences(null).contains(seq))
+ {
+ currentColor = Color.gray;
+ currentTextColor = Color.black;
+ }
+ else
+ {
+ currentColor = av.getSequenceColour(seq);
+ currentTextColor = Color.black;
+ }
+
+ pg.setColor(currentColor);
+ pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth, av
+ .getCharHeight());
+
+ pg.setColor(currentTextColor);
+
+ int xPos = 0;
+ if (av.rightAlignIds)
+ {
+ fm = pg.getFontMetrics();
+ xPos = idWidth
+ - fm.stringWidth(seq.getDisplayId(av.getShowJVSuffix()))
+ - 4;
+ }
+
+ pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos,
+ (((i - startSeq) * av.charHeight) + av.getCharHeight())
+ - (av.getCharHeight() / 5));
+ }
+
+ pg.setFont(av.getFont());
+
+ // draw main sequence panel
+ pg.translate(idWidth, 0);
+ seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
+
+ if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
+ {
+ pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
+ alabels.drawComponent((Graphics2D) pg, idWidth);
+ pg.translate(idWidth + 3, 0);
+ annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes + 1);
+ }
+
+ return Printable.PAGE_EXISTS;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pg
+ * DOCUMENT ME!
+ * @param pwidth
+ * DOCUMENT ME!
+ * @param pheight
+ * DOCUMENT ME!
+ * @param pi
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws PrinterException
+ * DOCUMENT ME!
+ */
+ public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
+ int pi) throws PrinterException
+ {
+
+ int annotationHeight = 0;
+ AnnotationLabels labels = null;
+ if (av.showAnnotation)
+ {
+ annotationHeight = annotationPanel.adjustPanelHeight();
+ labels = new AnnotationLabels(av);
+ }
+
+ int hgap = av.charHeight;
+ if (av.scaleAboveWrapped)
+ {
+ hgap += av.charHeight;
+ }
+
+ int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+ + annotationHeight;
+
+ int idWidth = getVisibleIdWidth();
+
+ int maxwidth = av.alignment.getWidth();
+ if (av.hasHiddenColumns)
+ {
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ }
+
+ int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth
+ - idWidth);
+
+ int totalHeight = cHeight * (maxwidth / resWidth + 1);
+
+ pg.setColor(Color.white);
+ pg.fillRect(0, 0, pwidth, pheight);
+ pg.setFont(av.getFont());
+
+ // //////////////
+ // Draw the ids
+ pg.setColor(Color.black);
+
+ pg.translate(0, -pi * pheight);
+
+ pg.setClip(0, pi * pheight, pwidth, pheight);
+
+ int ypos = hgap;
+
+ do
+ {
+ for (int i = 0; i < av.alignment.getHeight(); i++)
+ {
+ pg.setFont(idPanel.idCanvas.idfont);
+ SequenceI s = av.alignment.getSequenceAt(i);
+ String string = s.getDisplayId(av.getShowJVSuffix());
+ int xPos = 0;
+ if (av.rightAlignIds)
+ {
+ FontMetrics fm = pg.getFontMetrics();
+ xPos = idWidth - fm.stringWidth(string) - 4;
+ }
+ pg.drawString(string, xPos,
+ ((i * av.charHeight) + ypos + av.charHeight)
+ - (av.charHeight / 5));
+ }
+ if (labels != null)
+ {
+ pg.translate(-3, ypos
+ + (av.getAlignment().getHeight() * av.charHeight));
+
+ pg.setFont(av.getFont());
+ labels.drawComponent(pg, idWidth);
+ pg.translate(+3, -ypos
+ - (av.getAlignment().getHeight() * av.charHeight));
+ }
+
+ ypos += cHeight;
+ } while (ypos < totalHeight);
+
+ pg.translate(idWidth, 0);
+
+ seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight,
+ 0);
+
+ if ((pi * pheight) < totalHeight)
+ {
+ return Printable.PAGE_EXISTS;
+
+ }
+ else
+ {
+ return Printable.NO_SUCH_PAGE;
+ }
+ }
+
+ int getVisibleIdWidth()
+ {
+ return idPanel.getWidth() > 0 ? idPanel.getWidth()
+ : calculateIdWidth().width + 4;
+ }
+
+ void makeAlignmentImage(int type, File file)
+ {
+ int maxwidth = av.alignment.getWidth();
+ if (av.hasHiddenColumns)
+ {
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
+ }
+
+ int height = ((av.alignment.getHeight() + 1) * av.charHeight)
+ + scalePanel.getHeight();
+ int width = getVisibleIdWidth() + (maxwidth * av.charWidth);
+
+ if (av.getWrapAlignment())
+ {
+ height = getWrappedHeight();
+ if (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true"))
+ {
+ width = alignFrame.getWidth() - vscroll.getPreferredSize().width
+ - alignFrame.getInsets().left
+ - alignFrame.getInsets().right;
+ }
+ else
+ {
+ width = seqPanel.getWidth() + getVisibleIdWidth();
+ }
+
+ }
+ else if (av.getShowAnnotation())
+ {
+ height += annotationPanel.adjustPanelHeight() + 3;
+ }
+
+ try
+ {
+
+ jalview.util.ImageMaker im;
+ if (type == jalview.util.ImageMaker.PNG)
+ {
+ im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
+ "Create PNG image from alignment", width, height, file,
+ null);
+ }
+ else
+ {
+ im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
+ "Create EPS file from alignment", width, height, file,
+ alignFrame.getTitle());
+ }
+
+ if (av.getWrapAlignment())
+ {
+ if (im.getGraphics() != null)
+ {
+ printWrappedAlignment(im.getGraphics(), width, height, 0);
+ im.writeImage();
+ }
+ }
+ else
+ {
+ if (im.getGraphics() != null)
+ {
+ printUnwrapped(im.getGraphics(), width, height, 0);
+ im.writeImage();
+ }
+ }
+ } catch (OutOfMemoryError err)
+ {
+ // Be noisy here.
+ System.out.println("########################\n" + "OUT OF MEMORY "
+ + file + "\n" + "########################");
+ new OOMWarning("Creating Image for " + file, err);
+ // System.out.println("Create IMAGE: " + err);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void makeEPS(File epsFile)
+ {
+ makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void makePNG(File pngFile)
+ {
+ makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
+ }
+
+ public void makePNGImageMap(File imgMapFile, String imageName)
+ {
+ // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
+ // ////////////////////////////////////////////
+ int idWidth = getVisibleIdWidth();
+ FontMetrics fm = getFontMetrics(av.getFont());
+ int scaleHeight = av.charHeight + fm.getDescent();
+
+ // Gen image map
+ // ////////////////////////////////
+ if (imgMapFile != null)
+ {
+ try
+ {
+ int s, sSize = av.alignment.getHeight(), res, alwidth = av.alignment
+ .getWidth(), g, gSize, f, fSize, sy;
+ StringBuffer text = new StringBuffer();
+ PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
+ out.println(jalview.io.HTMLOutput.getImageMapHTML());
+ out.println("![](\"")
"
+ + "