X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=fae6dfc9fcd149b2d14ac019c5abb6eb31591050;hb=7e129811d6ff01074428462284dffc2a6c2395a4;hp=7a8a811bb519747b7166daf3ed754611f662d52b;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 7a8a811..fae6dfc 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,712 +1,1057 @@
/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
package jalview.gui;
-import jalview.jbgui.GAlignmentPanel;
-import jalview.schemes.*;
-import jalview.analysis.*;
import jalview.datamodel.*;
+
+import jalview.jbgui.*;
+
+import jalview.schemes.*;
+
+import org.jibble.epsgraphics.*;
+
import java.awt.*;
import java.awt.event.*;
+import java.awt.image.*;
import java.awt.print.*;
+
import java.io.*;
-import java.awt.image.*;
-import org.jibble.epsgraphics.*;
+
import javax.imageio.*;
-import javax.swing.*;
+import javax.swing.*;
-public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignmentPanel extends GAlignmentPanel
+ implements AdjustmentListener, Printable
{
+ 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);
- 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);
+ scalePanel = new ScalePanel(av, this);
- idPanelHolder.add(idPanel, BorderLayout.CENTER);
- idwidthAdjuster = new IdwidthAdjuster(this);
- idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
+ idPanelHolder.add(idPanel, BorderLayout.CENTER);
+ idwidthAdjuster = new IdwidthAdjuster(this);
+ idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
- annotationPanel = new AnnotationPanel(this);
- alabels = new AnnotationLabels(this);
+ annotationPanel = new AnnotationPanel(this);
+ alabels = new AnnotationLabels(this);
- annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());
- annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
- annotationScroller.setViewportView(annotationPanel);
- annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
+ annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());
+ annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
+ annotationScroller.setViewportView(annotationPanel);
+ annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
- fontChanged();
+ fontChanged();
- scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
- seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
+ scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
+ seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
- setScrollValues(0, 0);
+ setScrollValues(0, 0);
- hscroll.addAdjustmentListener(this);
- vscroll.addAdjustmentListener(this);
+ 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();
- }
+ setFocusable(true);
+ addKeyListener(new KeyAdapter()
+ {
+ public void keyPressed(KeyEvent evt)
+ {
+ switch (evt.getKeyCode())
+ {
+ case 27: // escape key
+ av.setSelectionGroup(null);
+ repaint();
- FontMetrics fm = g.getFontMetrics(av.font);
- AlignmentI al = av.getAlignment();
+ break;
- 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++;
- }
+ case KeyEvent.VK_DOWN:
+ alignFrame.moveSelectedSequences(false);
- // 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++;
- }
- }
+ break;
- return new Dimension(idWidth, 12);
- }
+ case KeyEvent.VK_UP:
+ alignFrame.moveSelectedSequences(true);
+ break;
- public void highlightSearchResults(int [] results)
- {
- seqPanel.seqCanvas.highlightSearchResults( results );
+ case KeyEvent.VK_BACK_SPACE:
+ case KeyEvent.VK_DELETE:
+ alignFrame.cut_actionPerformed(null);
+ break;
+ }
- // 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]);
+ }
+ });
}
- }
-
+ /**
+ * DOCUMENT ME!
+ */
+ public void fontChanged()
+ {
+ // set idCanvas bufferedImage to null
+ // to prevent drawing old image
+ FontMetrics fm = getFontMetrics(av.getFont());
- public OverviewPanel getOverviewPanel()
- {
- return overviewPanel;
- }
+ scalePanelHolder.setPreferredSize(new Dimension(10,
+ av.charHeight + fm.getDescent()));
+ idSpaceFillerPanel1.setPreferredSize(new Dimension(10,
+ av.charHeight + fm.getDescent()));
- public void setOverviewPanel(OverviewPanel op)
- {
- overviewPanel = op;
- }
+ 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);
- public void setAnnotationVisible(boolean b)
- {
- annotationSpaceFillerHolder.setVisible(b);
- annotationScroller.setVisible(b);
- }
+ 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());
+ }
+ if(overviewPanel!=null)
+ overviewPanel.setBoxPosition();
- public void setWrapAlignment(boolean wrap)
- {
- scalePanelHolder.setVisible(!wrap);
- hscroll.setVisible(!wrap);
- idwidthAdjuster.setVisible(!wrap);
+ repaint();
+ }
- av.setShowAnnotation(!wrap);
- annotationScroller.setVisible(!wrap);
- annotationSpaceFillerHolder.setVisible(!wrap);
- idSpaceFillerPanel1.setVisible(!wrap);
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Dimension calculateIdWidth()
+ {
+ Container c = new Container();
- repaint();
+ FontMetrics fm = c.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++;
+ }
- public void setColourScheme()
- {
- ColourSchemeI cs = av.getGlobalColourScheme();
+ // Also check annotation label widths
+ i = 0;
- if(av.getConservationSelected())
- {
+ if (al.getAlignmentAnnotation() != null)
+ {
+ fm = c.getFontMetrics(alabels.getFont());
- Alignment al = (Alignment)av.getAlignment();
- Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3, al.getSequences(), 0,
- al.getWidth() );
+ while (i < al.getAlignmentAnnotation().length)
+ {
+ String label = al.getAlignmentAnnotation()[i].label;
- c.calculate();
- c.verdict(false, av.ConsPercGaps);
- ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
+ if (fm.stringWidth(label) > idWidth)
+ {
+ idWidth = fm.stringWidth(label);
+ }
- av.setGlobalColourScheme( ccs );
+ i++;
+ }
+ }
+ return new Dimension(idWidth, 12);
}
- repaint();
- }
-
-
- int hextent = 0;
- int vextent = 0;
-
- // return value is true if the scroll is valid
- public boolean scrollUp(boolean up)
- {
- if(up)
+ /**
+ * DOCUMENT ME!
+ *
+ * @param results DOCUMENT ME!
+ */
+ public void highlightSearchResults(int[] results)
{
- if(vscroll.getValue()<1)
- return false;
- fastPaint = false;
- vscroll.setValue(vscroll.getValue() - 1);
+ 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]);
+ }
+ }
}
- else
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public OverviewPanel getOverviewPanel()
{
- if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())
- return false;
- fastPaint = false;
- vscroll.setValue(vscroll.getValue() + 1);
+ return overviewPanel;
}
- fastPaint = true;
- return true;
- }
- public boolean scrollRight(boolean right)
- {
-
- if (right)
+ /**
+ * DOCUMENT ME!
+ *
+ * @param op DOCUMENT ME!
+ */
+ public void setOverviewPanel(OverviewPanel op)
{
- if (hscroll.getValue() < 1)
- return false;
- fastPaint = false;
- hscroll.setValue(hscroll.getValue() - 1);
+ overviewPanel = op;
}
- else
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b DOCUMENT ME!
+ */
+ public void setAnnotationVisible(boolean b)
{
- if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
- return false;
- fastPaint = false;
- hscroll.setValue(hscroll.getValue() + 1);
+ annotationSpaceFillerHolder.setVisible(b);
+ annotationScroller.setVisible(b);
}
- fastPaint = true;
- return true;
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param wrap DOCUMENT ME!
+ */
+ public void setWrapAlignment(boolean wrap)
+ {
+ av.startSeq = 0;
+ scalePanelHolder.setVisible(!wrap);
+ hscroll.setVisible(!wrap);
+ idwidthAdjuster.setVisible(!wrap);
- 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(wrap)
+ {
+ annotationScroller.setVisible(false);
+ annotationSpaceFillerHolder.setVisible(false);
+ }
+ else if(av.showAnnotation)
+ {
+ annotationScroller.setVisible(true);
+ annotationSpaceFillerHolder.setVisible(true);
+ }
- if(hextent > av.alignment.getWidth())
- hextent = av.alignment.getWidth();
- if(vextent > av.alignment.getHeight())
- vextent = av.alignment.getHeight();
+ idSpaceFillerPanel1.setVisible(!wrap);
- if(hextent+x > av.getAlignment().getWidth())
- x = av.getAlignment().getWidth()- hextent;
+ repaint();
+ }
- if(vextent+y > av.getAlignment().getHeight())
- y = av.getAlignment().getHeight() - vextent;
- if(y<0)
- y = 0;
+ // return value is true if the scroll is valid
+ public boolean scrollUp(boolean up)
+ {
+ if (up)
+ {
+ if (vscroll.getValue() < 1)
+ {
+ return false;
+ }
- if(x<0)
- x=0;
+ fastPaint = false;
+ vscroll.setValue(vscroll.getValue() - 1);
+ }
+ else
+ {
+ if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
+ {
+ return false;
+ }
- hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
- vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
+ 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;
+ }
- public void adjustmentValueChanged(AdjustmentEvent evt)
- {
- int oldX = av.getStartRes();
- int oldY = av.getStartSeq();
+ fastPaint = false;
+ hscroll.setValue(hscroll.getValue() + 1);
+ }
- if (evt.getSource() == hscroll)
- {
- int x = hscroll.getValue();
- av.setStartRes(x);
- av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
- }
+ fastPaint = true;
- 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());
- }
+ return true;
}
- if(overviewPanel!=null)
- overviewPanel.setBoxPosition();
-
- if(av.getWrapAlignment() || !fastPaint)
- repaint();
- else
+ /**
+ * DOCUMENT ME!
+ *
+ * @param x DOCUMENT ME!
+ * @param y DOCUMENT ME!
+ */
+ public void setScrollValues(int x, int y)
{
- idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
- seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
- av.getStartSeq() - oldY);
+ av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -
+ 1);
- scalePanel.repaint();
- if (av.getShowAnnotation())
- annotationPanel.fastPaint(av.getStartRes() - oldX);
- }
+ 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();
+ }
- public void paintComponent(Graphics g)
- {
- invalidate();
- Dimension d = idPanel.idCanvas.getPreferredSize();
- idPanelHolder.setPreferredSize(d);
- hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
- validate();
+ if ((hextent + x) > av.getAlignment().getWidth())
+ {
+ x = av.getAlignment().getWidth() - hextent;
+ }
- 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());
- }
+ 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 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();
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void adjustmentValueChanged(AdjustmentEvent evt)
+ {
- if (av.getWrapAlignment())
- return printWrappedAlignment(pg, pwidth,pheight, pi);
- else
- return printUnwrapped(pg,pwidth, pheight,pi);
- }
+ int oldX = av.getStartRes();
+ int oldY = av.getStartSeq();
- public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
- {
+ if (evt.getSource() == hscroll)
+ {
+ int x = hscroll.getValue();
+ av.setStartRes(x);
+ av.setEndRes((x +
+ (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
+ }
- int idWidth = calculateIdWidth().width + 4;
- FontMetrics fm = getFontMetrics(av.getFont());
- int scaleHeight = av.charHeight + fm.getDescent();
+ 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()));
+ }
+ }
- pg.setColor(Color.white);
- pg.fillRect(0, 0, pwidth, pheight);
- pg.setFont(av.getFont());
+ if (overviewPanel != null)
+ {
+ overviewPanel.setBoxPosition();
+ }
- ////////////////////////////////////
- /// How many sequences and residues can we fit on a printable page?
- int totalRes = (pwidth - idWidth) / av.getCharWidth();
+ int xShift = av.getStartRes() - oldX;
+ int yShift = av.getStartSeq() - oldY;
- int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) - 1;
+ if ( (xShift == 0 && yShift == 0) ||
+ (Math.abs(xShift) > av.getEndRes() - av.getStartRes()
+ || Math.abs(yShift) > av.getEndSeq() - av.getStartSeq())
+ || av.getWrapAlignment()
+ || !fastPaint)
+ {
+ // Either no shift at all, or shift greater than visible amount
+ repaint();
+ }
+ else
+ {
+ idPanel.idCanvas.fastPaint(yShift);
+ seqPanel.seqCanvas.fastPaint(xShift, yShift);
- int pagesWide = av.getAlignment().getWidth() / totalRes + 1;
+ scalePanel.repaint();
- /////////////////////////////
- /// 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;
+ if (av.getShowAnnotation())
+ {
+ annotationPanel.fastPaint(xShift);
+ }
+ }
+ }
- startSeq = (pi / pagesWide) * totalSeq;
- endSeq = startSeq + totalSeq;
- if (endSeq > av.getAlignment().getHeight())
- endSeq = av.getAlignment().getHeight();
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g DOCUMENT ME!
+ */
+ public void paintComponent(Graphics g)
+ {
+ invalidate();
- int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
+ Dimension d = idPanel.idCanvas.getPreferredSize();
+ idPanelHolder.setPreferredSize(d);
+ hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
+ validate();
- if (av.showAnnotation)
- pagesHigh += annotationPanel.getHeight();
+ 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());
+ }
+ }
- pagesHigh /= pheight;
+ /**
+ * 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());
- if (pi >= pagesWide * pagesHigh)
- return Printable.NO_SUCH_PAGE;
+ int pwidth = (int) pf.getImageableWidth();
+ int pheight = (int) pf.getImageableHeight();
- //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)))
+ if (av.getWrapAlignment())
{
- currentColor = Color.gray;
- currentTextColor = Color.black;
+ return printWrappedAlignment(pg, pwidth, pheight, pi);
}
else
{
- currentColor = av.getAlignment().getSequenceAt(i).getColor();
- currentTextColor = Color.black;
+ return printUnwrapped(pg, pwidth, pheight, pi);
}
+ }
- pg.setColor(currentColor);
- pg.fillRect(0,
- jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,
- av.getCharHeight()),
- idWidth,
- av.getCharHeight());
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pg DOCUMENT ME!
+ * @param pwidth DOCUMENT ME!
+ * @param pheight DOCUMENT ME!
+ * @param pi DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws PrinterException DOCUMENT ME!
+ */
+ public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
+ throws PrinterException
+ {
+ int idWidth = calculateIdWidth().width + 4;
+ FontMetrics fm = getFontMetrics(av.getFont());
+ int scaleHeight = av.charHeight + fm.getDescent();
- pg.setColor(currentTextColor);
+ pg.setColor(Color.white);
+ pg.fillRect(0, 0, pwidth, pheight);
+ pg.setFont(av.getFont());
- String string = av.getAlignment().getSequenceAt(i).getName();
- if (av.getShowFullId())
- string = av.getAlignment().getSequenceAt(i).getDisplayId();
+ ////////////////////////////////////
+ /// How many sequences and residues can we fit on a printable page?
+ int totalRes = (pwidth - idWidth) / av.getCharWidth();
- pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight
- (startSeq, i, av.getCharHeight()) + av.getCharHeight() -
- (av.getCharHeight() / 5));
- }
+ int totalSeq = (int) ((pheight - scaleHeight) / av.getCharHeight()) -
+ 1;
- // draw main sequence panel
- pg.translate(idWidth, 0);
- seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,
- startRes, startSeq, 0);
+ int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
+ /////////////////////////////
+ /// Only print these sequences and residues on this page
+ int startRes;
- 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);
- }
+ /////////////////////////////
+ /// Only print these sequences and residues on this page
+ int endRes;
- return Printable.PAGE_EXISTS;
+ /////////////////////////////
+ /// 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;
+ }
- public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
- {
- int idWidth = calculateIdWidth().width + 4;
+ startSeq = (pi / pagesWide) * totalSeq;
+ endSeq = startSeq + totalSeq;
+
+ if (endSeq > av.getAlignment().getHeight())
+ {
+ endSeq = av.getAlignment().getHeight();
+ }
- int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth - idWidth);
- int totalHeight = totalHeight = (av.alignment.getHeight() + 2) *
- ( (av.alignment.getWidth()
- / resWidth) + 1) * av.charHeight;
+ int pagesHigh = ((av.alignment.getHeight() / totalSeq) + 1) * pheight;
+ if (av.showAnnotation)
+ {
+ pagesHigh += annotationPanel.getHeight();
+ }
- pg.setColor(Color.white);
- pg.fillRect(0, 0, pwidth, pheight);
- pg.setFont(av.getFont());
+ pagesHigh /= pheight;
- ////////////////
- // Draw the ids
- pg.setColor(Color.black);
+ if (pi >= (pagesWide * pagesHigh))
+ {
+ return Printable.NO_SUCH_PAGE;
+ }
- pg.translate(0, -pi * pheight);
+ //draw Scale
+ pg.translate(idWidth, 0);
+ scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
+ pg.translate(-idWidth, scaleHeight);
- pg.setClip(0,pi*pheight,pwidth, pheight);
+ ////////////////
+ // Draw the ids
+ Color currentColor = null;
+ Color currentTextColor = null;
- int ypos = 2 * av.charHeight;
- do
- {
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ for (int i = startSeq; i < endSeq; i++)
{
- SequenceI s = av.alignment.getSequenceAt(i);
- String string = s.getName();
- if (av.getShowFullId())
- string = s.getDisplayId();
+ 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, (i-startSeq) * av.charHeight, idWidth,
+ av.getCharHeight());
+
+ pg.setColor(currentTextColor);
+
+ String string = av.getAlignment().getSequenceAt(i).getName();
+
+ if (av.getShowFullId())
+ {
+ string = av.getAlignment().getSequenceAt(i).getDisplayId();
+ }
+
+ pg.drawString(string, 0,
+ (((i-startSeq) * av.charHeight) + av.getCharHeight()) -
+ (av.getCharHeight() / 5));
+ }
- pg.drawString(string, 0,
- AlignmentUtil.getPixelHeight(0, i, av.charHeight) +
- ypos +
- av.charHeight - (av.charHeight / 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);
}
- ypos += (av.alignment.getHeight() + 2) * av.charHeight;
+ return Printable.PAGE_EXISTS;
+ }
- }
- while (ypos < totalHeight);
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pg DOCUMENT ME!
+ * @param pwidth DOCUMENT ME!
+ * @param pheight DOCUMENT ME!
+ * @param pi DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws PrinterException DOCUMENT ME!
+ */
+ public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
+ int pi) throws PrinterException
+ {
+ int idWidth = calculateIdWidth().width + 4;
- pg.translate(idWidth, 0);
+ int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
+ idWidth);
+ int totalHeight = totalHeight = (av.alignment.getHeight() + 2) * ((av.alignment.getWidth() / resWidth) +
+ 1) * av.charHeight;
- seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
+ pg.setColor(Color.white);
+ pg.fillRect(0, 0, pwidth, pheight);
+ pg.setFont(av.getFont());
- if (pi * pheight < totalHeight)
- return Printable.PAGE_EXISTS;
- else
- return Printable.NO_SUCH_PAGE;
+ ////////////////
+ // 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,
+ ((i * av.charHeight) + ypos + av.charHeight) -
+ (av.charHeight / 5));
+ }
+
+ ypos += ((av.alignment.getHeight() + 2) * av.charHeight);
+ }
+ while (ypos < totalHeight);
- public void makeEPS()
- {
- int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;
- int width = seqPanel.getWidth() + idPanel.getWidth();
+ pg.translate(idWidth, 0);
- if (!av.getWrapAlignment())
- {
- height = (av.alignment.getHeight()+1) * av.charHeight + 30;
- width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
+ seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
+
+ if ((pi * pheight) < totalHeight)
+ {
+ return Printable.PAGE_EXISTS;
+ }
+ else
+ {
+ return Printable.NO_SUCH_PAGE;
+ }
}
- if(av.getShowAnnotation())
- {
- height += annotationPanel.getPreferredSize().height;
- }
- try
+ /**
+ * DOCUMENT ME!
+ */
+ public void makeEPS(File epsFile)
{
- 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(epsFile == null)
+ {
+ 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;
+ }
+
+ epsFile = chooser.getSelectedFile();
+
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ chooser.getSelectedFile().getParent());
+ }
+
+ int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
+ int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
if (av.getWrapAlignment())
- printWrappedAlignment(pg, width, height, 0);
- else
- printUnwrapped(pg, width, height, 0);
+ {
+ height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *
+ av.chunkHeight;
+ width = seqPanel.getWidth() + idPanel.getWidth();
+ }
+
+
+ if (av.getShowAnnotation())
+ {
+ height += annotationPanel.getPreferredSize().height;
+ }
- pg.flush();
- pg.close();
+ try
+ {
+ FileOutputStream out = new FileOutputStream(epsFile);
+ 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();
+ }
}
- catch (Exception ex)
+
+
+ public void makePNGImageMap(File imgMapFile, String imageName)
{
- ex.printStackTrace();
- }
- }
+ ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
+ //////////////////////////////////////////////
+ int idWidth = calculateIdWidth().width + 4;
+ FontMetrics fm = getFontMetrics(av.getFont());
+ int scaleHeight = av.charHeight + fm.getDescent();
- public void makePNG()
- {
- int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;
- int width = seqPanel.getWidth() + idPanel.getWidth();
+ // Gen image map
+ //////////////////////////////////
+ if(imgMapFile!=null)
+ {
+ try
+ {
+ PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
+ out.println(jalview.io.HTMLOutput.getImageMapHTML());
+ out.println("
"
+ +"