X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=60ef4801d2ce461ff2ab3ae4ccac68c5ebd4ad1d;hb=48eba1af1959565659fae9f9e7f4e28d9726c28c;hp=1a48af6fbe1471e03fd96d4fbbb6dc0825674cb5;hpb=6e71f42b0a3713ddbc3054e7ea9d8f5088130ec9;p=jalview.git
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
old mode 100755
new mode 100644
index 1a48af6..60ef480
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,821 +1,1788 @@
-/*
- * 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 java.io.*;
-import javax.imageio.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-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
-{
- 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;
- 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);
-
- 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();
- }
-
- // 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;
-
- /////////////////////////////
- /// 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.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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.analysis.AnnotationSorter;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.HTMLOutput;
+import jalview.jbgui.GAlignmentPanel;
+import jalview.math.AlignmentDimension;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.print.PageFormat;
+import java.awt.print.Printable;
+import java.awt.print.PrinterException;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.PrintWriter;
+import java.util.List;
+
+import javax.swing.SwingUtilities;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision: 1.161 $
+ */
+public class AlignmentPanel extends GAlignmentPanel implements
+ AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI
+{
+ public AlignViewport av;
+
+ OverviewPanel overviewPanel;
+
+ private SeqPanel seqPanel;
+
+ private IdPanel idPanel;
+
+ private boolean headless;
+
+ IdwidthAdjuster idwidthAdjuster;
+
+ /** DOCUMENT ME!! */
+ public AlignFrame alignFrame;
+
+ private ScalePanel scalePanel;
+
+ private AnnotationPanel annotationPanel;
+
+ private AnnotationLabels alabels;
+
+ private int hextent = 0;
+
+ private int vextent = 0;
+
+ /*
+ * Flag set while scrolling to follow complementary cDNA/protein scroll. When
+ * false, suppresses invoking the same method recursively.
+ */
+ private boolean scrollComplementaryPanel = true;
+
+ private PropertyChangeListener propertyChangeListener;
+
+ private CalculationChooser calculationDialog;
+
+ /**
+ * Creates a new AlignmentPanel object.
+ *
+ * @param af
+ * @param av
+ */
+ public AlignmentPanel(AlignFrame af, final AlignViewport av)
+ {
+ alignFrame = af;
+ this.av = av;
+ setSeqPanel(new SeqPanel(av, this));
+ setIdPanel(new IdPanel(av, this));
+
+ setScalePanel(new ScalePanel(av, this));
+
+ idPanelHolder.add(getIdPanel(), BorderLayout.CENTER);
+ idwidthAdjuster = new IdwidthAdjuster(this);
+ idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
+
+ setAnnotationPanel(new AnnotationPanel(this));
+ setAlabels(new AnnotationLabels(this));
+
+ annotationScroller.setViewportView(getAnnotationPanel());
+ annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER);
+
+ scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER);
+ seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER);
+
+ setScrollValues(0, 0);
+
+ hscroll.addAdjustmentListener(this);
+ vscroll.addAdjustmentListener(this);
+
+ addComponentListener(new ComponentAdapter()
+ {
+ @Override
+ public void componentResized(ComponentEvent evt)
+ {
+ // reset the viewport ranges when the alignment panel is resized
+ // in particular, this initialises the end residue value when Jalview
+ // is initialised
+ ViewportRanges ranges = av.getRanges();
+ if (av.getWrapAlignment())
+ {
+ int widthInRes = getSeqPanel().seqCanvas.getWrappedCanvasWidth(
+ getSeqPanel().seqCanvas.getWidth());
+ ranges.setViewportWidth(widthInRes);
+ }
+ else
+ {
+ int widthInRes = getSeqPanel().seqCanvas.getWidth()
+ / av.getCharWidth();
+ int heightInSeq = getSeqPanel().seqCanvas.getHeight()
+ / av.getCharHeight();
+
+ ranges.setViewportWidth(widthInRes);
+ ranges.setViewportHeight(heightInSeq);
+ }
+ }
+
+ });
+
+ final AlignmentPanel ap = this;
+ propertyChangeListener = new PropertyChangeListener()
+ {
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ if (evt.getPropertyName().equals("alignment"))
+ {
+ PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
+ alignmentChanged();
+ }
+ }
+ };
+ av.addPropertyChangeListener(propertyChangeListener);
+
+ av.getRanges().addPropertyChangeListener(this);
+ fontChanged();
+ adjustAnnotationHeight();
+ updateLayout();
+ }
+
+ @Override
+ public AlignViewportI getAlignViewport()
+ {
+ return av;
+ }
+
+ public void alignmentChanged()
+ {
+ av.alignmentChanged(this);
+
+ if (getCalculationDialog() != null)
+ {
+ getCalculationDialog().validateCalcTypes();
+ }
+
+ alignFrame.updateEditMenuBar();
+
+ // no idea if we need to update structure
+ paintAlignment(true, true);
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void fontChanged()
+ {
+ // set idCanvas bufferedImage to null
+ // to prevent drawing old image
+ FontMetrics fm = getFontMetrics(av.getFont());
+
+ scalePanelHolder.setPreferredSize(
+ new Dimension(10, av.getCharHeight() + fm.getDescent()));
+ idSpaceFillerPanel1.setPreferredSize(
+ new Dimension(10, av.getCharHeight() + fm.getDescent()));
+ idwidthAdjuster.invalidate();
+ scalePanelHolder.invalidate();
+ getIdPanel().getIdCanvas().gg = null;
+ getSeqPanel().seqCanvas.img = null;
+ getAnnotationPanel().adjustPanelHeight();
+
+ Dimension d = calculateIdWidth();
+
+ d.setSize(d.width + 4, d.height);
+ getIdPanel().getIdCanvas().setPreferredSize(d);
+ hscrollFillerPanel.setPreferredSize(d);
+
+ repaint();
+ }
+
+ /**
+ * Calculate the width of the alignment labels based on the displayed names
+ * and any bounds on label width set in preferences.
+ *
+ * @return Dimension giving the maximum width of the alignment label panel
+ * that should be used.
+ */
+ public Dimension calculateIdWidth()
+ {
+ // calculate sensible default width when no preference is available
+ Dimension r = null;
+ if (av.getIdWidth() < 0)
+ {
+ int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
+ int maxwidth = Math.max(20, Math.min(afwidth - 200, 2 * afwidth / 3));
+ r = calculateIdWidth(maxwidth);
+ av.setIdWidth(r.width);
+ }
+ else
+ {
+ r = new Dimension();
+ r.width = av.getIdWidth();
+ r.height = 0;
+ }
+ return r;
+ }
+
+ /**
+ * Calculate the width of the alignment labels based on the displayed names
+ * and any bounds on label width set in preferences.
+ *
+ * @param maxwidth
+ * -1 or maximum width allowed for IdWidth
+ * @return Dimension giving the maximum width of the alignment label panel
+ * that should be used.
+ */
+ public Dimension calculateIdWidth(int maxwidth)
+ {
+ Container c = new Container();
+
+ FontMetrics fm = c.getFontMetrics(
+ new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
+
+ AlignmentI al = av.getAlignment();
+ int i = 0;
+ int idWidth = 0;
+ String id;
+
+ while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
+ {
+ SequenceI s = al.getSequenceAt(i);
+
+ id = s.getDisplayId(av.getShowJVSuffix());
+
+ if (fm.stringWidth(id) > idWidth)
+ {
+ idWidth = fm.stringWidth(id);
+ }
+
+ i++;
+ }
+
+ // Also check annotation label widths
+ i = 0;
+
+ if (al.getAlignmentAnnotation() != null)
+ {
+ fm = c.getFontMetrics(getAlabels().getFont());
+
+ while (i < al.getAlignmentAnnotation().length)
+ {
+ String label = al.getAlignmentAnnotation()[i].label;
+
+ if (fm.stringWidth(label) > idWidth)
+ {
+ idWidth = fm.stringWidth(label);
+ }
+
+ i++;
+ }
+ }
+
+ return new Dimension(
+ maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth), 12);
+ }
+
+ /**
+ * Highlight the given results on the alignment.
+ *
+ */
+ public void highlightSearchResults(SearchResultsI results)
+ {
+ boolean scrolled = scrollToPosition(results, 0, true, false);
+
+ boolean noFastPaint = scrolled && av.getWrapAlignment();
+
+ getSeqPanel().seqCanvas.highlightSearchResults(results, noFastPaint);
+ }
+
+ /**
+ * Scroll the view to show the position of the highlighted region in results
+ * (if any)
+ *
+ * @param searchResults
+ * @param redrawOverview
+ * @return
+ */
+ public boolean scrollToPosition(SearchResultsI searchResults,
+ boolean redrawOverview)
+ {
+ return scrollToPosition(searchResults, 0, redrawOverview, false);
+ }
+
+ /**
+ * Scrolls the view (if necessary) to show the position of the first
+ * highlighted region in results (if any). Answers true if the view was
+ * scrolled, or false if no matched region was found, or it is already
+ * visible.
+ *
+ * @param results
+ * @param verticalOffset
+ * if greater than zero, allows scrolling to a position below the
+ * first displayed sequence
+ * @param redrawOverview
+ * - when set, the overview will be recalculated (takes longer)
+ * @param centre
+ * if true, try to centre the search results horizontally in the view
+ * @return
+ */
+ protected boolean scrollToPosition(SearchResultsI results,
+ int verticalOffset, boolean redrawOverview, boolean centre)
+ {
+ int startv, endv, starts, ends;
+ ViewportRanges ranges = av.getRanges();
+
+ if (results == null || results.isEmpty() || av == null
+ || av.getAlignment() == null)
+ {
+ return false;
+ }
+ int seqIndex = av.getAlignment().findIndex(results);
+ if (seqIndex == -1)
+ {
+ return false;
+ }
+ SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
+
+ int[] r = results.getResults(seq, 0, av.getAlignment().getWidth());
+ if (r == null)
+ {
+ return false;
+ }
+ int start = r[0];
+ int end = r[1];
+
+ /*
+ * To centre results, scroll to positions half the visible width
+ * left/right of the start/end positions
+ */
+ if (centre)
+ {
+ int offset = (ranges.getEndRes() - ranges.getStartRes() + 1) / 2 - 1;
+ start = Math.max(start - offset, 0);
+ end = end + offset - 1;
+ }
+ if (start < 0)
+ {
+ return false;
+ }
+ if (end == seq.getEnd())
+ {
+ return false;
+ }
+
+ if (av.hasHiddenColumns())
+ {
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ start = hidden.absoluteToVisibleColumn(start);
+ end = hidden.absoluteToVisibleColumn(end);
+ if (start == end)
+ {
+ if (!hidden.isVisible(r[0]))
+ {
+ // don't scroll - position isn't visible
+ return false;
+ }
+ }
+ }
+
+ /*
+ * allow for offset of target sequence (actually scroll to one above it)
+ */
+ seqIndex = Math.max(0, seqIndex - verticalOffset);
+ boolean scrollNeeded = true;
+
+ if (!av.getWrapAlignment())
+ {
+ if ((startv = ranges.getStartRes()) >= start)
+ {
+ /*
+ * Scroll left to make start of search results visible
+ */
+ setScrollValues(start, seqIndex);
+ }
+ else if ((endv = ranges.getEndRes()) <= end)
+ {
+ /*
+ * Scroll right to make end of search results visible
+ */
+ setScrollValues(startv + end - endv, seqIndex);
+ }
+ else if ((starts = ranges.getStartSeq()) > seqIndex)
+ {
+ /*
+ * Scroll up to make start of search results visible
+ */
+ setScrollValues(ranges.getStartRes(), seqIndex);
+ }
+ else if ((ends = ranges.getEndSeq()) <= seqIndex)
+ {
+ /*
+ * Scroll down to make end of search results visible
+ */
+ setScrollValues(ranges.getStartRes(), starts + seqIndex - ends
+ + 1);
+ }
+ /*
+ * Else results are already visible - no need to scroll
+ */
+ scrollNeeded = false;
+ }
+ else
+ {
+ scrollNeeded = ranges.scrollToWrappedVisible(start);
+ }
+
+ paintAlignment(redrawOverview, false);
+
+ return scrollNeeded;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public OverviewPanel getOverviewPanel()
+ {
+ return overviewPanel;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param op
+ * DOCUMENT ME!
+ */
+ public void setOverviewPanel(OverviewPanel op)
+ {
+ overviewPanel = op;
+ }
+
+ /**
+ *
+ * @param b
+ * Hide or show annotation panel
+ *
+ */
+ public void setAnnotationVisible(boolean b)
+ {
+ if (!av.getWrapAlignment())
+ {
+ annotationSpaceFillerHolder.setVisible(b);
+ annotationScroller.setVisible(b);
+ }
+ repaint();
+ }
+
+ /**
+ * automatically adjust annotation panel height for new annotation whilst
+ * ensuring the alignment is still visible.
+ */
+ @Override
+ public void adjustAnnotationHeight()
+ {
+ // TODO: display vertical annotation scrollbar if necessary
+ // this is called after loading new annotation onto alignment
+ if (alignFrame.getHeight() == 0)
+ {
+ System.out.println("NEEDS FIXING");
+ }
+ validateAnnotationDimensions(true);
+ addNotify();
+ // TODO: many places call this method and also paintAlignment with various
+ // different settings. this means multiple redraws are triggered...
+ paintAlignment(true, false);
+ }
+
+ /**
+ * calculate the annotation dimensions and refresh slider values accordingly.
+ * need to do repaints/notifys afterwards.
+ */
+ protected void validateAnnotationDimensions(boolean adjustPanelHeight)
+ {
+ int annotationHeight = getAnnotationPanel().adjustPanelHeight();
+ annotationHeight = getAnnotationPanel()
+ .adjustForAlignFrame(adjustPanelHeight, annotationHeight);
+
+ hscroll.addNotify();
+ annotationScroller.setPreferredSize(
+ new Dimension(annotationScroller.getWidth(), annotationHeight));
+
+ Dimension e = idPanel.getSize();
+ alabels.setSize(new Dimension(e.width, annotationHeight));
+
+ annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+ annotationSpaceFillerHolder.getWidth(), annotationHeight));
+ annotationScroller.validate();
+ annotationScroller.addNotify();
+ }
+
+ /**
+ * update alignment layout for viewport settings
+ *
+ * @param wrap
+ * DOCUMENT ME!
+ */
+ public void updateLayout()
+ {
+ fontChanged();
+ setAnnotationVisible(av.isShowAnnotation());
+ boolean wrap = av.getWrapAlignment();
+ ViewportRanges ranges = av.getRanges();
+ ranges.setStartSeq(0);
+ scalePanelHolder.setVisible(!wrap);
+ hscroll.setVisible(!wrap);
+ idwidthAdjuster.setVisible(!wrap);
+
+ if (wrap)
+ {
+ annotationScroller.setVisible(false);
+ annotationSpaceFillerHolder.setVisible(false);
+ }
+ else if (av.isShowAnnotation())
+ {
+ annotationScroller.setVisible(true);
+ annotationSpaceFillerHolder.setVisible(true);
+ validateAnnotationDimensions(false);
+ }
+
+ int canvasWidth = getSeqPanel().seqCanvas.getWidth();
+ if (canvasWidth > 0)
+ { // may not yet be laid out
+ if (wrap)
+ {
+ int widthInRes = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(canvasWidth);
+ ranges.setViewportWidth(widthInRes);
+ }
+ else
+ {
+ int widthInRes = (canvasWidth / av.getCharWidth());
+ int heightInSeq = (getSeqPanel().seqCanvas.getHeight()
+ / av.getCharHeight());
+
+ ranges.setViewportWidth(widthInRes);
+ ranges.setViewportHeight(heightInSeq);
+ }
+ }
+
+ idSpaceFillerPanel1.setVisible(!wrap);
+
+ repaint();
+ }
+
+ /**
+ * Adjust row/column scrollers to show a visible position in the alignment.
+ *
+ * @param x
+ * visible column to scroll to
+ * @param y
+ * visible row to scroll to
+ *
+ */
+ public void setScrollValues(int xpos, int ypos)
+ {
+ int x = xpos;
+ int y = ypos;
+
+ if (av == null || av.getAlignment() == null)
+ {
+ return;
+ }
+
+ if (av.getWrapAlignment())
+ {
+ setScrollingForWrappedPanel(x);
+ }
+ else
+ {
+ int width = av.getAlignment().getWidth();
+ int height = av.getAlignment().getHeight();
+
+ if (av.hasHiddenColumns())
+ {
+ // reset the width to exclude hidden columns
+ width = av.getAlignment().getHiddenColumns()
+ .absoluteToVisibleColumn(width);
+ }
+
+ hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
+ vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
+
+ if (hextent > width)
+ {
+ hextent = width;
+ }
+
+ if (vextent > height)
+ {
+ vextent = height;
+ }
+
+ if ((hextent + x) > width)
+ {
+ x = width - hextent;
+ }
+
+ if ((vextent + y) > height)
+ {
+ y = height - vextent;
+ }
+
+ if (y < 0)
+ {
+ y = 0;
+ }
+
+ if (x < 0)
+ {
+ x = 0;
+ }
+
+ // update the scroll values
+ hscroll.setValues(x, hextent, 0, width);
+ vscroll.setValues(y, vextent, 0, height);
+ }
+ }
+
+ /**
+ * Respond to adjustment event when horizontal or vertical scrollbar is
+ * changed
+ *
+ * @param evt
+ * adjustment event encoding whether hscroll or vscroll changed
+ */
+ @Override
+ public void adjustmentValueChanged(AdjustmentEvent evt)
+ {
+ if (av.getWrapAlignment())
+ {
+ adjustScrollingWrapped(evt);
+ return;
+ }
+
+ ViewportRanges ranges = av.getRanges();
+
+ if (evt.getSource() == hscroll)
+ {
+ int oldX = ranges.getStartRes();
+ int oldwidth = ranges.getViewportWidth();
+ int x = hscroll.getValue();
+ int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
+
+ // if we're scrolling to the position we're already at, stop
+ // this prevents infinite recursion of events when the scroll/viewport
+ // ranges values are the same
+ if ((x == oldX) && (width == oldwidth))
+ {
+ return;
+ }
+ ranges.setViewportStartAndWidth(x, width);
+ }
+ else if (evt.getSource() == vscroll)
+ {
+ int oldY = ranges.getStartSeq();
+ int oldheight = ranges.getViewportHeight();
+ int y = vscroll.getValue();
+ int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
+
+ // if we're scrolling to the position we're already at, stop
+ // this prevents infinite recursion of events when the scroll/viewport
+ // ranges values are the same
+ if ((y == oldY) && (height == oldheight))
+ {
+ return;
+ }
+ ranges.setViewportStartAndHeight(y, height);
+ }
+ repaint();
+ }
+
+ /**
+ * Responds to a scroll change by setting the start position of the viewport.
+ * Does
+ *
+ * @param evt
+ */
+ protected void adjustScrollingWrapped(AdjustmentEvent evt)
+ {
+ if (evt.getSource() == hscroll)
+ {
+ return; // no horizontal scroll when wrapped
+ }
+ final ViewportRanges ranges = av.getRanges();
+
+ if (evt.getSource() == vscroll)
+ {
+ int newY = vscroll.getValue();
+
+ /*
+ * if we're scrolling to the position we're already at, stop
+ * this prevents infinite recursion of events when the scroll/viewport
+ * ranges values are the same
+ */
+ int oldX = ranges.getStartRes();
+ int oldY = ranges.getWrappedScrollPosition(oldX);
+ if (oldY == newY)
+ {
+ return;
+ }
+ if (newY > -1)
+ {
+ /*
+ * limit page up/down to one width's worth of positions
+ */
+ int rowSize = ranges.getViewportWidth();
+ int newX = newY > oldY ? oldX + rowSize : oldX - rowSize;
+ ranges.setViewportStartAndWidth(Math.max(0, newX), 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()
+ {
+ @Override
+ public void run()
+ {
+ // When updating scrolling to use ViewportChange events, this code
+ // could not be validated and it is not clear if it is now being
+ // called. Log warning here in case it is called and unforeseen
+ // problems occur
+ Cache.log.warn(
+ "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
+
+ // scroll to start of panel
+ ranges.setStartRes(0);
+ ranges.setStartSeq(0);
+ }
+ });
+ }
+ repaint();
+ }
+
+ /* (non-Javadoc)
+ * @see jalview.api.AlignmentViewPanel#paintAlignment(boolean)
+ */
+ @Override
+ public void paintAlignment(boolean updateOverview,
+ boolean updateStructures)
+ {
+ final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
+ av.isShowAutocalculatedAbove());
+ sorter.sort(getAlignment().getAlignmentAnnotation(),
+ av.getSortAnnotationsBy());
+ repaint();
+
+ if (updateStructures)
+ {
+ av.getStructureSelectionManager().sequenceColoursChanged(this);
+ }
+ if (updateOverview)
+ {
+
+ if (overviewPanel != null)
+ {
+ overviewPanel.updateOverviewImage();
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ */
+ @Override
+ public void paintComponent(Graphics g)
+ {
+ invalidate(); // needed so that the id width adjuster works correctly
+
+ Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
+ idPanelHolder.setPreferredSize(d);
+ hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
+
+ validate(); // needed so that the id width adjuster works correctly
+
+ /*
+ * set scroll bar positions - tried to remove but necessary for split panel to resize correctly
+ * though I still think this call should be elsewhere.
+ */
+ ViewportRanges ranges = av.getRanges();
+ setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
+ }
+
+ /**
+ * Set vertical scroll bar position, and number of increments, for wrapped
+ * panel
+ *
+ * @param topLeftColumn
+ * the column position at top left (0..)
+ */
+ private void setScrollingForWrappedPanel(int topLeftColumn)
+ {
+ ViewportRanges ranges = av.getRanges();
+ int scrollPosition = ranges.getWrappedScrollPosition(topLeftColumn);
+ int maxScroll = ranges.getWrappedMaxScroll(topLeftColumn);
+
+ /*
+ * a scrollbar's value can be set to at most (maximum-extent)
+ * so we add extent (1) to the maxScroll value
+ */
+ vscroll.setUnitIncrement(1);
+ vscroll.setValues(scrollPosition, 1, 0, maxScroll + 1);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pg
+ * DOCUMENT ME!
+ * @param pf
+ * DOCUMENT ME!
+ * @param pi
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws PrinterException
+ * DOCUMENT ME!
+ */
+ @Override
+ 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(pwidth, pheight, pi, pg);
+ }
+ else
+ {
+ return printUnwrapped(pwidth, pheight, pi, pg, pg);
+ }
+ }
+
+ /**
+ * Draws the alignment image, including sequence ids, sequences, and
+ * annotation labels and annotations if shown, on either one or two Graphics
+ * contexts.
+ *
+ * @param pageWidth
+ * in pixels
+ * @param pageHeight
+ * in pixels
+ * @param pageIndex
+ * (0, 1, ...)
+ * @param idGraphics
+ * the graphics context for sequence ids and annotation labels
+ * @param alignmentGraphics
+ * the graphics context for sequences and annotations (may or may not
+ * be the same context as idGraphics)
+ * @return
+ * @throws PrinterException
+ */
+ public int printUnwrapped(int pageWidth, int pageHeight, int pageIndex,
+ Graphics idGraphics, Graphics alignmentGraphics)
+ throws PrinterException
+ {
+ final int idWidth = getVisibleIdWidth(false);
+
+ /*
+ * Get the horizontal offset to where we draw the sequences.
+ * This is idWidth if using a single Graphics context, else zero.
+ */
+ final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0
+ : idWidth;
+
+ FontMetrics fm = getFontMetrics(av.getFont());
+ final int charHeight = av.getCharHeight();
+ final int scaleHeight = charHeight + fm.getDescent();
+
+ idGraphics.setColor(Color.white);
+ idGraphics.fillRect(0, 0, pageWidth, pageHeight);
+ idGraphics.setFont(av.getFont());
+
+ /*
+ * How many sequences and residues can we fit on a printable page?
+ */
+ final int totalRes = (pageWidth - idWidth) / av.getCharWidth();
+
+ final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
+
+ final int alignmentWidth = av.getAlignment().getWidth();
+ final int pagesWide = (alignmentWidth / totalRes) + 1;
+
+ final int startRes = (pageIndex % pagesWide) * totalRes;
+ final int endRes = Math.min(startRes + totalRes - 1,
+ alignmentWidth - 1);
+
+ final int startSeq = (pageIndex / pagesWide) * totalSeq;
+ final int alignmentHeight = av.getAlignment().getHeight();
+ final int endSeq = Math.min(startSeq + totalSeq, alignmentHeight);
+
+ int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight;
+
+ if (av.isShowAnnotation())
+ {
+ pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
+ }
+
+ pagesHigh /= pageHeight;
+
+ if (pageIndex >= (pagesWide * pagesHigh))
+ {
+ return Printable.NO_SUCH_PAGE;
+ }
+ final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + 3;
+
+ /*
+ * draw the Scale at horizontal offset, then reset to top left (0, 0)
+ */
+ alignmentGraphics.translate(alignmentGraphicsOffset, 0);
+ getScalePanel().drawScale(alignmentGraphics, startRes, endRes,
+ pageWidth - idWidth, scaleHeight);
+ alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
+
+ /*
+ * Draw the sequence ids, offset for scale height,
+ * then reset to top left (0, 0)
+ */
+ idGraphics.translate(0, scaleHeight);
+ IdCanvas idCanvas = getIdPanel().getIdCanvas();
+ List selection = av.getSelectionGroup() == null ? null
+ : av.getSelectionGroup().getSequences(null);
+ idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1,
+ selection);
+
+ idGraphics.setFont(av.getFont());
+ idGraphics.translate(0, -scaleHeight);
+
+ /*
+ * draw the sequences, offset for scale height, and id width (if using a
+ * single graphics context), then reset to (0, scale height)
+ */
+ alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
+ getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes,
+ endRes, startSeq, endSeq - 1);
+ alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
+
+ if (av.isShowAnnotation() && (endSeq == alignmentHeight))
+ {
+ /*
+ * draw annotation labels; drawComponent() translates by
+ * getScrollOffset(), so compensate for that first;
+ * then reset to (0, scale height)
+ */
+ int offset = getAlabels().getScrollOffset();
+ idGraphics.translate(0, -offset);
+ idGraphics.translate(0, alignmentDrawnHeight);
+ getAlabels().drawComponent(idGraphics, idWidth);
+ idGraphics.translate(0, -alignmentDrawnHeight);
+
+ /*
+ * draw the annotations starting at
+ * (idOffset, alignmentHeight) from (0, scaleHeight)
+ */
+ alignmentGraphics.translate(alignmentGraphicsOffset,
+ alignmentDrawnHeight);
+ getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
+ alignmentGraphics, -1, startRes, endRes + 1);
+ }
+
+ return Printable.PAGE_EXISTS;
+ }
+
+ /**
+ * Prints one page of an alignment in wrapped mode. Returns
+ * Printable.PAGE_EXISTS (0) if a page was drawn, or Printable.NO_SUCH_PAGE if
+ * no page could be drawn (page number out of range).
+ *
+ * @param pageWidth
+ * @param pageHeight
+ * @param pageNumber
+ * (0, 1, ...)
+ * @param g
+ *
+ * @return
+ *
+ * @throws PrinterException
+ */
+ public int printWrappedAlignment(int pageWidth, int pageHeight, int pageNumber,
+ Graphics g) throws PrinterException
+ {
+ int annotationHeight = 0;
+ if (av.isShowAnnotation())
+ {
+ annotationHeight = getAnnotationPanel().adjustPanelHeight();
+ }
+
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
+ {
+ hgap += av.getCharHeight();
+ }
+
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
+ + annotationHeight;
+
+ int idWidth = getVisibleIdWidth(false);
+
+ int maxwidth = av.getAlignment().getWidth();
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .absoluteToVisibleColumn(maxwidth) - 1;
+ }
+
+ int resWidth = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(pageWidth - idWidth);
+
+ int totalHeight = cHeight * (maxwidth / resWidth + 1);
+
+ g.setColor(Color.white);
+ g.fillRect(0, 0, pageWidth, pageHeight);
+ g.setFont(av.getFont());
+ g.setColor(Color.black);
+
+ /*
+ * method: print the whole wrapped alignment, but with a clip region that
+ * is restricted to the requested page; this supports selective print of
+ * single pages or ranges, (at the cost of some repeated processing in
+ * the 'normal' case, when all pages are printed)
+ */
+ g.translate(0, -pageNumber * pageHeight);
+
+ g.setClip(0, pageNumber * pageHeight, pageWidth, pageHeight);
+
+ /*
+ * draw sequence ids and annotation labels (if shown)
+ */
+ IdCanvas idCanvas = getIdPanel().getIdCanvas();
+ idCanvas.drawIdsWrapped((Graphics2D) g, av, 0, totalHeight);
+
+ g.translate(idWidth, 0);
+
+ getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, pageWidth - idWidth,
+ totalHeight, 0);
+
+ if ((pageNumber * pageHeight) < totalHeight)
+ {
+ return Printable.PAGE_EXISTS;
+ }
+ else
+ {
+ return Printable.NO_SUCH_PAGE;
+ }
+ }
+
+ /**
+ * get current sequence ID panel width, or nominal value if panel were to be
+ * displayed using default settings
+ *
+ * @return
+ */
+ public int getVisibleIdWidth()
+ {
+ return getVisibleIdWidth(true);
+ }
+
+ /**
+ * get current sequence ID panel width, or nominal value if panel were to be
+ * displayed using default settings
+ *
+ * @param onscreen
+ * indicate if the Id width for onscreen or offscreen display should
+ * be returned
+ * @return
+ */
+ public int getVisibleIdWidth(boolean onscreen)
+ {
+ // see if rendering offscreen - check preferences and calc width accordingly
+ if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
+ {
+ return calculateIdWidth(-1).width + 4;
+ }
+ Integer idwidth = null;
+ if (onscreen || (idwidth = Cache
+ .getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
+ {
+ int w = getIdPanel().getWidth();
+ return (w > 0 ? w : calculateIdWidth().width + 4);
+ }
+ return idwidth.intValue() + 4;
+ }
+
+ void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
+ {
+ int boarderBottomOffset = 5;
+ long pSessionId = System.currentTimeMillis();
+ headless = (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true"));
+ if (alignFrame != null && !headless)
+ {
+ if (file != null)
+ {
+ alignFrame.setProgressBar(MessageManager
+ .formatMessage("status.saving_file", new Object[]
+ { type.getLabel() }), pSessionId);
+ }
+ }
+ try
+ {
+ AlignmentDimension aDimension = getAlignmentDimension();
+ try
+ {
+ jalview.util.ImageMaker im;
+ final String imageAction, imageTitle;
+ if (type == jalview.util.ImageMaker.TYPE.PNG)
+ {
+ imageAction = "Create PNG image from alignment";
+ imageTitle = null;
+ }
+ else if (type == jalview.util.ImageMaker.TYPE.EPS)
+ {
+ imageAction = "Create EPS file from alignment";
+ imageTitle = alignFrame.getTitle();
+ }
+ else
+ {
+ imageAction = "Create SVG file from alignment";
+ imageTitle = alignFrame.getTitle();
+ }
+
+ im = new jalview.util.ImageMaker(this, type, imageAction,
+ aDimension.getWidth(),
+ aDimension.getHeight() + boarderBottomOffset, file,
+ imageTitle, alignFrame, pSessionId, headless);
+ Graphics graphics = im.getGraphics();
+ if (av.getWrapAlignment())
+ {
+ if (graphics != null)
+ {
+ printWrappedAlignment(aDimension.getWidth(),
+ aDimension.getHeight() + boarderBottomOffset, 0,
+ graphics);
+ im.writeImage();
+ }
+ }
+ else
+ {
+ if (graphics != null)
+ {
+ printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
+ graphics, graphics);
+ im.writeImage();
+ }
+ }
+
+ } catch (OutOfMemoryError err)
+ {
+ // Be noisy here.
+ System.out.println("########################\n" + "OUT OF MEMORY "
+ + file + "\n" + "########################");
+ new OOMWarning("Creating Image for " + file, err);
+ // System.out.println("Create IMAGE: " + err);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ } finally
+ {
+
+ }
+ }
+
+ public AlignmentDimension getAlignmentDimension()
+ {
+ int maxwidth = av.getAlignment().getWidth();
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .absoluteToVisibleColumn(maxwidth);
+ }
+
+ int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
+ + getScalePanel().getHeight();
+ int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
+
+ if (av.getWrapAlignment())
+ {
+ height = getWrappedHeight();
+ if (headless)
+ {
+ // need to obtain default alignment width and then add in any
+ // additional allowance for id margin
+ // this duplicates the calculation in getWrappedHeight but adjusts for
+ // offscreen idWith
+ width = alignFrame.getWidth() - vscroll.getPreferredSize().width
+ - alignFrame.getInsets().left - alignFrame.getInsets().right
+ - getVisibleIdWidth() + getVisibleIdWidth(false);
+ }
+ else
+ {
+ width = getSeqPanel().getWidth() + getVisibleIdWidth(false);
+ }
+
+ }
+ else if (av.isShowAnnotation())
+ {
+ height += getAnnotationPanel().adjustPanelHeight() + 3;
+ }
+ return new AlignmentDimension(width, height);
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void makeEPS(File epsFile)
+ {
+ makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void makePNG(File pngFile)
+ {
+ makeAlignmentImage(jalview.util.ImageMaker.TYPE.PNG, pngFile);
+ }
+
+ public void makeSVG(File svgFile)
+ {
+ makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
+ }
+
+ public void makePNGImageMap(File imgMapFile, String imageName)
+ {
+ // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
+ // ////////////////////////////////////////////
+ int idWidth = getVisibleIdWidth(false);
+ FontMetrics fm = getFontMetrics(av.getFont());
+ int scaleHeight = av.getCharHeight() + fm.getDescent();
+
+ // Gen image map
+ // ////////////////////////////////
+ if (imgMapFile != null)
+ {
+ try
+ {
+ int sSize = av.getAlignment().getHeight();
+ int alwidth = av.getAlignment().getWidth();
+ PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
+ out.println(HTMLOutput.getImageMapHTML());
+ out.println(""
+ + "