X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=e4a4c906af87e827554036a375df8868630d117f;hb=cca50cb3aee94f3ed1a5e504d45b8d8b665f8c5b;hp=cdff8a3a65f5cd2af3698584dfe2df65819db439;hpb=890bd0eac47a4b0f55bd062a359c16a43c3780a0;p=jalview.git
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
old mode 100755
new mode 100644
index cdff8a3..e4a4c90
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,1203 +1,1627 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package jalview.gui;
-
-import java.beans.*;
-import java.io.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.print.*;
-import javax.swing.*;
-
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class AlignmentPanel
- extends GAlignmentPanel implements AdjustmentListener, Printable
-{
- public AlignViewport av;
- OverviewPanel overviewPanel;
- SeqPanel seqPanel;
- IdPanel idPanel;
- IdwidthAdjuster idwidthAdjuster;
-
- /** DOCUMENT ME!! */
- public AlignFrame alignFrame;
- ScalePanel scalePanel;
- AnnotationPanel annotationPanel;
- AnnotationLabels alabels;
-
- // this value is set false when selection area being dragged
- boolean fastPaint = true;
- int hextent = 0;
- int vextent = 0;
-
- /**
- * Creates a new AlignmentPanel object.
- *
- * @param af DOCUMENT ME!
- * @param av DOCUMENT ME!
- */
- public AlignmentPanel(AlignFrame af, final AlignViewport av)
- {
- alignFrame = af;
- this.av = av;
- seqPanel = new SeqPanel(av, this);
- idPanel = new IdPanel(av, this);
-
- scalePanel = new ScalePanel(av, this);
-
- idPanelHolder.add(idPanel, BorderLayout.CENTER);
- idwidthAdjuster = new IdwidthAdjuster(this);
- idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
-
- annotationPanel = new AnnotationPanel(this);
- alabels = new AnnotationLabels(this);
-
- annotationScroller.setViewportView(annotationPanel);
- annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
-
- fontChanged();
-
- 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();
- }
- }
- });
-
- adjustAnnotationHeight();
-
- }
-
- public void alignmentChanged()
- {
- av.alignmentChanged(this);
-
- if (overviewPanel != null)
- {
- overviewPanel.updateOverviewImage();
- }
-
- alignFrame.updateEditMenuBar();
-
- repaint();
- }
-
- /**
- * DOCUMENT ME!
- */
- public void fontChanged()
- {
- // set idCanvas bufferedImage to null
- // to prevent drawing old image
- FontMetrics fm = getFontMetrics(av.getFont());
-
- scalePanelHolder.setPreferredSize(new Dimension(10,
- av.charHeight + fm.getDescent()));
- idSpaceFillerPanel1.setPreferredSize(new Dimension(10,
- av.charHeight + fm.getDescent()));
-
- idPanel.idCanvas.gg = null;
- seqPanel.seqCanvas.img = null;
- annotationPanel.adjustPanelHeight();
-
- Dimension d = calculateIdWidth();
- d.setSize(d.width + 4, d.height);
- idPanel.idCanvas.setPreferredSize(d);
- hscrollFillerPanel.setPreferredSize(d);
-
- if (overviewPanel != null)
- {
- overviewPanel.setBoxPosition();
- }
-
- repaint();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Dimension calculateIdWidth()
- {
- Container c = new Container();
-
- FontMetrics fm = c.getFontMetrics(
- new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
-
- AlignmentI al = av.getAlignment();
-
- int i = 0;
- int idWidth = 0;
- String id;
-
- while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null))
- {
- SequenceI s = al.getSequenceAt(i);
-
- id = s.getDisplayId(av.getShowJVSuffix());
-
- if (fm.stringWidth(id) > idWidth)
- {
- idWidth = fm.stringWidth(id);
- }
-
- i++;
- }
-
- // Also check annotation label widths
- i = 0;
-
- if (al.getAlignmentAnnotation() != null)
- {
- fm = c.getFontMetrics(alabels.getFont());
-
- while (i < al.getAlignmentAnnotation().length)
- {
- String label = al.getAlignmentAnnotation()[i].label;
-
- if (fm.stringWidth(label) > idWidth)
- {
- idWidth = fm.stringWidth(label);
- }
-
- i++;
- }
- }
-
- return new Dimension(idWidth, 12);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param results DOCUMENT ME!
- */
- public void highlightSearchResults(SearchResults results)
- {
- seqPanel.seqCanvas.highlightSearchResults(results);
-
- // do we need to scroll the panel?
- if (results != null)
- {
- SequenceI seq = results.getResultSequence(0);
- int seqIndex = av.alignment.findIndex(seq);
- int start = seq.findIndex(results.getResultStart(0)) - 1;
- int end = seq.findIndex(results.getResultEnd(0)) - 1;
-
- if (!av.wrapAlignment)
- {
- if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||
- ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
- {
- setScrollValues(start, seqIndex);
- }
- }
- else
- {
- scrollToWrappedVisible(start);
- }
- }
- }
-
- void scrollToWrappedVisible(int res)
- {
- int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.
- getWidth());
- if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
- {
- vscroll.setValue(res / cwidth);
- av.startRes = vscroll.getValue() * cwidth;
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public OverviewPanel getOverviewPanel()
- {
- return overviewPanel;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param op DOCUMENT ME!
- */
- public void setOverviewPanel(OverviewPanel op)
- {
- overviewPanel = op;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
- */
- public void setAnnotationVisible(boolean b)
- {
- if (!av.wrapAlignment)
- {
- annotationSpaceFillerHolder.setVisible(b);
- annotationScroller.setVisible(b);
- }
- repaint();
- }
-
- public void adjustAnnotationHeight()
- {
- if (alignFrame.getHeight() == 0)
- {
- System.out.println("NEEDS FIXING");
- }
-
- int height = annotationPanel.adjustPanelHeight();
-
- if (height > alignFrame.getHeight() / 2)
- {
- height = alignFrame.getHeight() / 2;
- }
-
- annotationScroller.setPreferredSize(
- new Dimension(annotationScroller.getWidth(),
- height));
-
- annotationSpaceFillerHolder.setPreferredSize(new Dimension(
- annotationSpaceFillerHolder.getWidth(),
- height));
-
- repaint();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param wrap DOCUMENT ME!
- */
- public void setWrapAlignment(boolean wrap)
- {
- av.startSeq = 0;
- scalePanelHolder.setVisible(!wrap);
- hscroll.setVisible(!wrap);
- idwidthAdjuster.setVisible(!wrap);
-
- if (wrap)
- {
- annotationScroller.setVisible(false);
- annotationSpaceFillerHolder.setVisible(false);
- }
- else if (av.showAnnotation)
- {
- annotationScroller.setVisible(true);
- annotationSpaceFillerHolder.setVisible(true);
- }
-
- idSpaceFillerPanel1.setVisible(!wrap);
-
- repaint();
- }
-
- // return value is true if the scroll is valid
- public boolean scrollUp(boolean up)
- {
- if (up)
- {
- if (vscroll.getValue() < 1)
- {
- return false;
- }
-
- fastPaint = false;
- vscroll.setValue(vscroll.getValue() - 1);
- }
- else
- {
- if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
- {
- return false;
- }
-
- fastPaint = false;
- vscroll.setValue(vscroll.getValue() + 1);
- }
-
- fastPaint = true;
-
- return true;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param right DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean scrollRight(boolean right)
- {
- if (!right)
- {
- if (hscroll.getValue() < 1)
- {
- return false;
- }
-
- fastPaint = false;
- hscroll.setValue(hscroll.getValue() - 1);
- }
- else
- {
- if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
- {
- return false;
- }
-
- fastPaint = false;
- hscroll.setValue(hscroll.getValue() + 1);
- }
-
- fastPaint = true;
-
- return true;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param x DOCUMENT ME!
- * @param y DOCUMENT ME!
- */
- public void setScrollValues(int x, int y)
- {
-
- int width = av.alignment.getWidth();
- int height = av.alignment.getHeight();
-
- if (av.hasHiddenColumns)
- {
- width = av.getColumnSelection().findColumnPosition(width);
- }
-
- av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) - 1);
-
- hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
- vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
-
- if (hextent > width)
- {
- hextent = width;
- }
-
- if (vextent > height)
- {
- vextent = height;
- }
-
- if ( (hextent + x) > width)
- {
- x = width - hextent;
- }
-
- if ( (vextent + y) > height)
- {
- y = height - vextent;
- }
-
- if (y < 0)
- {
- y = 0;
- }
-
- if (x < 0)
- {
- x = 0;
- }
-
- hscroll.setValues(x, hextent, 0, width);
- vscroll.setValues(y, vextent, 0, height);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void adjustmentValueChanged(AdjustmentEvent evt)
- {
-
- int oldX = av.getStartRes();
- int oldY = av.getStartSeq();
-
- if (evt.getSource() == hscroll)
- {
- int x = hscroll.getValue();
- av.setStartRes(x);
- av.setEndRes( (x +
- (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
- }
-
- if (evt.getSource() == vscroll)
- {
- int offy = vscroll.getValue();
-
- if (av.getWrapAlignment())
- {
- if (offy > -1)
- {
- int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
- seqCanvas.getWidth());
- av.setStartRes(offy * rowSize);
- av.setEndRes( (offy + 1) * rowSize);
- }
- else
- {
- //This is only called if file loaded is a jar file that
- //was wrapped when saved and user has wrap alignment true
- //as preference setting
- SwingUtilities.invokeLater(new Runnable()
- {
- public void run()
- {
- setScrollValues(av.getStartRes(), av.getStartSeq());
- }
- });
- }
- }
- else
- {
- av.setStartSeq(offy);
- av.setEndSeq(offy +
- (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
- }
- }
-
- if (overviewPanel != null)
- {
- overviewPanel.setBoxPosition();
- }
-
- int scrollX = av.startRes - oldX;
- int scrollY = av.startSeq - oldY;
-
- if (av.getWrapAlignment() || !fastPaint)
- {
- repaint();
- }
- else
- {
- // Make sure we're not trying to draw a panel
- // larger than the visible window
- if (scrollX > av.endRes - av.startRes)
- {
- scrollX = av.endRes - av.startRes;
- }
- else if (scrollX < av.startRes - av.endRes)
- {
- scrollX = av.startRes - av.endRes;
- }
-
- if (scrollX != 0 || scrollY != 0)
- {
- idPanel.idCanvas.fastPaint(scrollY);
- seqPanel.seqCanvas.fastPaint(scrollX,
- scrollY);
- scalePanel.repaint();
-
- if (av.getShowAnnotation())
- {
- annotationPanel.fastPaint(scrollX);
- }
- }
- }
- }
-
- public void paintAlignment(boolean updateOverview)
- {
- repaint();
-
- if(updateOverview)
- {
- jalview.structure.StructureSelectionManager.getStructureSelectionManager()
- .sequenceColoursChanged(this);
-
- if (overviewPanel != null)
- {
- overviewPanel.updateOverviewImage();
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- */
- public void paintComponent(Graphics g)
- {
- invalidate();
-
- Dimension d = idPanel.idCanvas.getPreferredSize();
- idPanelHolder.setPreferredSize(d);
- hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
- validate();
-
- if (av.getWrapAlignment())
- {
- int maxwidth = av.alignment.getWidth();
-
- if (av.hasHiddenColumns)
- {
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
- }
-
- int canvasWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
- seqCanvas.getWidth());
- if (canvasWidth > 0)
- {
- int max = maxwidth /
- seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.
- getWidth()) +
- 1;
- vscroll.setMaximum(max);
- vscroll.setUnitIncrement(1);
- vscroll.setVisibleAmount(1);
- }
- }
- else
- {
- setScrollValues(av.getStartRes(), av.getStartSeq());
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param pg DOCUMENT ME!
- * @param pf DOCUMENT ME!
- * @param pi DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- *
- * @throws PrinterException DOCUMENT ME!
- */
- public int print(Graphics pg, PageFormat pf, int pi)
- throws PrinterException
- {
- pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
-
- int pwidth = (int) pf.getImageableWidth();
- int pheight = (int) pf.getImageableHeight();
-
- if (av.getWrapAlignment())
- {
- return printWrappedAlignment(pg, pwidth, pheight, pi);
- }
- else
- {
- return printUnwrapped(pg, pwidth, pheight, pi);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param pg DOCUMENT ME!
- * @param pwidth DOCUMENT ME!
- * @param pheight DOCUMENT ME!
- * @param pi DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- *
- * @throws PrinterException DOCUMENT ME!
- */
- public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
- throws PrinterException
- {
- int idWidth = getVisibleIdWidth();
- FontMetrics fm = getFontMetrics(av.getFont());
- int scaleHeight = av.charHeight + fm.getDescent();
-
- pg.setColor(Color.white);
- pg.fillRect(0, 0, pwidth, pheight);
- pg.setFont(av.getFont());
-
- ////////////////////////////////////
- /// How many sequences and residues can we fit on a printable page?
- int totalRes = (pwidth - idWidth) / av.getCharWidth();
-
- int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) -
- 1;
-
- int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
-
- /////////////////////////////
- /// Only print these sequences and residues on this page
- int startRes;
-
- /////////////////////////////
- /// Only print these sequences and residues on this page
- int endRes;
-
- /////////////////////////////
- /// Only print these sequences and residues on this page
- int startSeq;
-
- /////////////////////////////
- /// Only print these sequences and residues on this page
- int endSeq;
- startRes = (pi % pagesWide) * totalRes;
- endRes = (startRes + totalRes) - 1;
-
- if (endRes > (av.getAlignment().getWidth() - 1))
- {
- endRes = av.getAlignment().getWidth() - 1;
- }
-
- startSeq = (pi / pagesWide) * totalSeq;
- endSeq = startSeq + totalSeq;
-
- if (endSeq > av.getAlignment().getHeight())
- {
- endSeq = av.getAlignment().getHeight();
- }
-
- int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
-
- if (av.showAnnotation)
- {
- pagesHigh += annotationPanel.adjustPanelHeight() + 3;
- }
-
- pagesHigh /= pheight;
-
- if (pi >= (pagesWide * pagesHigh))
- {
- return Printable.NO_SUCH_PAGE;
- }
-
- //draw Scale
- pg.translate(idWidth, 0);
- scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
- pg.translate( -idWidth, scaleHeight);
-
- ////////////////
- // Draw the ids
- Color currentColor = null;
- Color currentTextColor = null;
-
- pg.setFont(idPanel.idCanvas.idfont);
-
- SequenceI seq;
- for (int i = startSeq; i < endSeq; i++)
- {
- seq = av.getAlignment().getSequenceAt(i);
- if ( (av.getSelectionGroup() != null) &&
- av.getSelectionGroup().getSequences(null).contains(seq))
- {
- currentColor = Color.gray;
- currentTextColor = Color.black;
- }
- else
- {
- currentColor = av.getSequenceColour(seq);
- currentTextColor = Color.black;
- }
-
- pg.setColor(currentColor);
- pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
- av.getCharHeight());
-
- pg.setColor(currentTextColor);
-
- int xPos = 0;
- if (av.rightAlignIds)
- {
- fm = pg.getFontMetrics();
- xPos = idWidth - fm.stringWidth(
- seq.getDisplayId(av.getShowJVSuffix())
- ) - 4;
- }
-
- pg.drawString(seq.getDisplayId(av.getShowJVSuffix()),
- xPos,
- ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
- (av.getCharHeight() / 5));
- }
-
- pg.setFont(av.getFont());
-
- // draw main sequence panel
- pg.translate(idWidth, 0);
- seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
-
- if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
- {
- pg.translate( -idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
- alabels.drawComponent( (Graphics2D) pg, idWidth);
- pg.translate(idWidth + 3, 0);
- annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +
- 1);
- }
-
- return Printable.PAGE_EXISTS;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param pg DOCUMENT ME!
- * @param pwidth DOCUMENT ME!
- * @param pheight DOCUMENT ME!
- * @param pi DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- *
- * @throws PrinterException DOCUMENT ME!
- */
- public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
- int pi)
- throws PrinterException
- {
-
- int annotationHeight = 0;
- AnnotationLabels labels = null;
- if (av.showAnnotation)
- {
- annotationHeight = annotationPanel.adjustPanelHeight();
- labels = new AnnotationLabels(av);
- }
-
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
- {
- hgap += av.charHeight;
- }
-
- int cHeight = av.getAlignment().getHeight() * av.charHeight
- + hgap
- + annotationHeight;
-
- int idWidth = getVisibleIdWidth();
-
- int maxwidth = av.alignment.getWidth();
- if (av.hasHiddenColumns)
- {
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
- }
-
- int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
- idWidth);
-
- int totalHeight = cHeight * (maxwidth / resWidth + 1);
-
- pg.setColor(Color.white);
- pg.fillRect(0, 0, pwidth, pheight);
- pg.setFont(av.getFont());
-
- ////////////////
- // Draw the ids
- pg.setColor(Color.black);
-
- pg.translate(0, -pi * pheight);
-
- pg.setClip(0, pi * pheight, pwidth, pheight);
-
- int ypos = hgap;
-
- do
- {
- for (int i = 0; i < av.alignment.getHeight(); i++)
- {
- pg.setFont(idPanel.idCanvas.idfont);
- SequenceI s = av.alignment.getSequenceAt(i);
- String string = s.getDisplayId(av.getShowJVSuffix());
- int xPos = 0;
- if (av.rightAlignIds)
- {
- FontMetrics fm = pg.getFontMetrics();
- xPos = idWidth - fm.stringWidth(string) - 4;
- }
- pg.drawString(string, xPos,
- ( (i * av.charHeight) + ypos + av.charHeight) -
- (av.charHeight / 5));
- }
- if (labels != null)
- {
- pg.translate( -3,
- ypos +
- (av.getAlignment().getHeight() * av.charHeight));
-
- pg.setFont(av.getFont());
- labels.drawComponent(pg, idWidth);
- pg.translate( +3,
- -ypos -
- (av.getAlignment().getHeight() * av.charHeight));
- }
-
- ypos += cHeight;
- }
- while (ypos < totalHeight);
-
- pg.translate(idWidth, 0);
-
- seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
-
- if ( (pi * pheight) < totalHeight)
- {
- return Printable.PAGE_EXISTS;
-
- }
- else
- {
- return Printable.NO_SUCH_PAGE;
- }
- }
-
- int getVisibleIdWidth()
- {
- return
- idPanel.getWidth() > 0 ? idPanel.getWidth() :
- calculateIdWidth().width + 4;
- }
-
- void makeAlignmentImage(int type, File file)
- {
- int maxwidth = av.alignment.getWidth();
- if (av.hasHiddenColumns)
- {
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
- }
-
- int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
- int width = getVisibleIdWidth() + (maxwidth * av.charWidth);
-
- if (av.getWrapAlignment())
- {
- height = getWrappedHeight();
- if (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true"))
- {
- width = alignFrame.getWidth()
- - vscroll.getPreferredSize().width
- - alignFrame.getInsets().left
- - alignFrame.getInsets().right;
- }
- else
- {
- width = seqPanel.getWidth() + getVisibleIdWidth();
- }
-
- }
- else if (av.getShowAnnotation())
- {
- height += annotationPanel.adjustPanelHeight() + 3;
- }
-
- try
- {
-
- jalview.util.ImageMaker im;
- if (type == jalview.util.ImageMaker.PNG)
- {
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.PNG,
- "Create PNG image from alignment",
- width, height, file, null);
- }
- else
- {
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.EPS,
- "Create EPS file from alignment",
- width, height, file,
- alignFrame.getTitle());
- }
-
- if (av.getWrapAlignment())
- {
- if (im.getGraphics() != null)
- {
- printWrappedAlignment(im.getGraphics(), width, height, 0);
- im.writeImage();
- }
- }
- else
- {
- if (im.getGraphics() != null)
- {
- printUnwrapped(im.getGraphics(), width, height, 0);
- im.writeImage();
- }
- }
- }
- catch (OutOfMemoryError err)
- {
- System.out.println("########################\n"
- + "OUT OF MEMORY " + file + "\n"
- + "########################");
-
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Out of Memory Creating Image!!"
- +
- "\nSee help files for increasing Java Virtual Machine memory."
- , "Out of memory",
- JOptionPane.WARNING_MESSAGE);
- System.out.println("Create IMAGE: " + err);
- System.gc();
-
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- /**
- * DOCUMENT ME!
- */
- public void makeEPS(File epsFile)
- {
- makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
- }
-
- /**
- * DOCUMENT ME!
- */
- public void makePNG(File pngFile)
- {
- makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
- }
-
- public void makePNGImageMap(File imgMapFile, String imageName)
- {
- ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
- //////////////////////////////////////////////
- int idWidth = getVisibleIdWidth();
- FontMetrics fm = getFontMetrics(av.getFont());
- int scaleHeight = av.charHeight + fm.getDescent();
-
- // Gen image map
- //////////////////////////////////
- if (imgMapFile != null)
- {
- try
- {
- int s, sSize = av.alignment.getHeight(),
- res, alwidth = av.alignment.getWidth(), g, gSize, f, fSize, sy;
- StringBuffer text = new StringBuffer();
- PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
- out.println(jalview.io.HTMLOutput.getImageMapHTML());
- out.println(""
- + "