X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=fae6dfc9fcd149b2d14ac019c5abb6eb31591050;hb=7e129811d6ff01074428462284dffc2a6c2395a4;hp=068d605ba00d31b1772a21f3ea96e0f92d377e0b;hpb=71019ada6142e8a449dfcec0a9c87eb00efbefaf;p=jalview.git
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 068d605..fae6dfc 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -18,804 +18,1040 @@
*/
package jalview.gui;
-import java.io.*;
-import javax.imageio.*;
+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 javax.imageio.*;
+
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
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+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 = false;
- 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()
+ 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)
{
- public void keyPressed(KeyEvent evt)
- {
- switch (evt.getKeyCode())
- {
- case 27: // escape key
- av.setSelectionGroup(null);
- repaint();
+ alignFrame = af;
+ this.av = av;
+ seqPanel = new SeqPanel(av, this);
+ idPanel = new IdPanel(av, this);
- break;
+ scalePanel = new ScalePanel(av, this);
- case KeyEvent.VK_DOWN:
- alignFrame.moveSelectedSequences(false);
+ idPanelHolder.add(idPanel, BorderLayout.CENTER);
+ idwidthAdjuster = new IdwidthAdjuster(this);
+ idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
- break;
+ annotationPanel = new AnnotationPanel(this);
+ alabels = new AnnotationLabels(this);
- case KeyEvent.VK_UP:
- alignFrame.moveSelectedSequences(true);
+ annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());
+ annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
+ annotationScroller.setViewportView(annotationPanel);
+ annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
- 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();
- }
+ fontChanged();
- FontMetrics fm = g.getFontMetrics(av.font);
- AlignmentI al = av.getAlignment();
+ scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
+ seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
- int i = 0;
- int idWidth = 0;
- String id;
+ setScrollValues(0, 0);
- while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null))
- {
- SequenceI s = al.getSequenceAt(i);
+ hscroll.addAdjustmentListener(this);
+ vscroll.addAdjustmentListener(this);
- if (av.getShowFullId())
- {
- id = s.getDisplayId();
- }
- else
- {
- id = s.getName();
- }
+ setFocusable(true);
+ addKeyListener(new KeyAdapter()
+ {
+ public void keyPressed(KeyEvent evt)
+ {
+ switch (evt.getKeyCode())
+ {
+ case 27: // escape key
+ av.setSelectionGroup(null);
+ repaint();
- if (fm.stringWidth(id) > idWidth)
- {
- idWidth = fm.stringWidth(id);
- }
+ break;
- i++;
- }
+ case KeyEvent.VK_DOWN:
+ alignFrame.moveSelectedSequences(false);
- // Also check annotation label widths
- i = 0;
+ break;
- if (al.getAlignmentAnnotation() != null)
- {
- fm = g.getFontMetrics(alabels.getFont());
+ case KeyEvent.VK_UP:
+ alignFrame.moveSelectedSequences(true);
- while (i < al.getAlignmentAnnotation().length)
- {
- String label = al.getAlignmentAnnotation()[i].label;
+ break;
- if (fm.stringWidth(label) > idWidth)
- {
- idWidth = fm.stringWidth(label);
- }
+ case KeyEvent.VK_BACK_SPACE:
+ case KeyEvent.VK_DELETE:
+ alignFrame.cut_actionPerformed(null);
+ break;
+ }
- 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())
+ /**
+ * DOCUMENT ME!
+ */
+ public void fontChanged()
{
- Alignment al = (Alignment) av.getAlignment();
- Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3,
- al.getSequences(), 0,
- al.getWidth());
+ // set idCanvas bufferedImage to null
+ // to prevent drawing old image
+ FontMetrics fm = getFontMetrics(av.getFont());
- c.calculate();
- c.verdict(false, av.ConsPercGaps);
+ scalePanelHolder.setPreferredSize(new Dimension(10,
+ av.charHeight + fm.getDescent()));
+ idSpaceFillerPanel1.setPreferredSize(new Dimension(10,
+ av.charHeight + fm.getDescent()));
- ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
+ idPanel.idCanvas.gg = null;
+ seqPanel.seqCanvas.img = null;
+ annotationPanel.adjustPanelHeight();
- av.setGlobalColourScheme(ccs);
- }
+ Dimension d = calculateIdWidth();
+ d.setSize(d.width + 4, d.height);
+ idPanel.idCanvas.setPreferredSize(d);
+ hscrollFillerPanel.setPreferredSize(d);
- repaint();
- }
+ 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());
+ }
- // return value is true if the scroll is valid
- public boolean scrollUp(boolean up)
- {
- if (up)
- {
- if (vscroll.getValue() < 1)
- {
- return false;
- }
+ if(overviewPanel!=null)
+ overviewPanel.setBoxPosition();
- fastPaint = false;
- vscroll.setValue(vscroll.getValue() - 1);
+ repaint();
}
- else
- {
- if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
- {
- return false;
- }
- fastPaint = false;
- vscroll.setValue(vscroll.getValue() + 1);
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Dimension calculateIdWidth()
+ {
+ Container c = new Container();
- fastPaint = true;
+ FontMetrics fm = c.getFontMetrics(av.font);
+ AlignmentI al = av.getAlignment();
- return true;
- }
+ int i = 0;
+ int idWidth = 0;
+ String id;
- public boolean scrollRight(boolean right)
- {
- if (right)
- {
- if (hscroll.getValue() < 1)
- {
- return false;
- }
+ 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++;
+ }
- fastPaint = false;
- hscroll.setValue(hscroll.getValue() - 1);
- }
- else
- {
- if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
- {
- return false;
- }
+ // Also check annotation label widths
+ i = 0;
- fastPaint = false;
- hscroll.setValue(hscroll.getValue() + 1);
- }
+ if (al.getAlignmentAnnotation() != null)
+ {
+ fm = c.getFontMetrics(alabels.getFont());
- fastPaint = true;
+ while (i < al.getAlignmentAnnotation().length)
+ {
+ String label = al.getAlignmentAnnotation()[i].label;
- return true;
- }
+ if (fm.stringWidth(label) > idWidth)
+ {
+ idWidth = fm.stringWidth(label);
+ }
- public void setScrollValues(int x, int y)
- {
- av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -
- 1);
+ i++;
+ }
+ }
- hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
- vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
+ return new Dimension(idWidth, 12);
+ }
- if (hextent > av.alignment.getWidth())
+ /**
+ * DOCUMENT ME!
+ *
+ * @param results DOCUMENT ME!
+ */
+ public void highlightSearchResults(int[] results)
{
- hextent = av.alignment.getWidth();
+ 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]);
+ }
+ }
}
- if (vextent > av.alignment.getHeight())
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public OverviewPanel getOverviewPanel()
{
- vextent = av.alignment.getHeight();
+ return overviewPanel;
}
- if ( (hextent + x) > av.getAlignment().getWidth())
+ /**
+ * DOCUMENT ME!
+ *
+ * @param op DOCUMENT ME!
+ */
+ public void setOverviewPanel(OverviewPanel op)
{
- x = av.getAlignment().getWidth() - hextent;
+ overviewPanel = op;
}
- if ( (vextent + y) > av.getAlignment().getHeight())
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b DOCUMENT ME!
+ */
+ public void setAnnotationVisible(boolean b)
{
- y = av.getAlignment().getHeight() - vextent;
+ annotationSpaceFillerHolder.setVisible(b);
+ annotationScroller.setVisible(b);
}
- if (y < 0)
+ /**
+ * DOCUMENT ME!
+ *
+ * @param wrap DOCUMENT ME!
+ */
+ public void setWrapAlignment(boolean wrap)
{
- y = 0;
+ 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();
}
- if (x < 0)
+
+ // return value is true if the scroll is valid
+ public boolean scrollUp(boolean up)
{
- x = 0;
- }
+ 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;
+ }
- hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
- vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
- }
+ fastPaint = false;
+ vscroll.setValue(vscroll.getValue() + 1);
+ }
- public void adjustmentValueChanged(AdjustmentEvent evt)
- {
- int oldX = av.getStartRes();
- int oldY = av.getStartSeq();
+ fastPaint = true;
- if (evt.getSource() == hscroll)
- {
- int x = hscroll.getValue();
- av.setStartRes(x);
- av.setEndRes( (x +
- (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
+ return true;
}
- if (evt.getSource() == vscroll)
+ /**
+ * DOCUMENT ME!
+ *
+ * @param right DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean scrollRight(boolean right)
{
- int offy = vscroll.getValue();
+ if (right)
+ {
+ if (hscroll.getValue() < 1)
+ {
+ return false;
+ }
- 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()));
- }
- }
+ fastPaint = false;
+ hscroll.setValue(hscroll.getValue() - 1);
+ }
+ else
+ {
+ if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
+ {
+ return false;
+ }
- if (overviewPanel != null)
- {
- overviewPanel.setBoxPosition();
- }
+ fastPaint = false;
+ hscroll.setValue(hscroll.getValue() + 1);
+ }
- if (av.getWrapAlignment() || !fastPaint)
- {
- repaint();
+ fastPaint = true;
+
+ return true;
}
- 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();
+ hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
+ vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
- if (av.getShowAnnotation())
- {
- annotationPanel.fastPaint(av.getStartRes() - oldX);
- }
- }
- }
+ if (hextent > av.alignment.getWidth())
+ {
+ hextent = av.alignment.getWidth();
+ }
- public void paintComponent(Graphics g)
- {
- invalidate();
+ if (vextent > av.alignment.getHeight())
+ {
+ vextent = av.alignment.getHeight();
+ }
- 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;
+ }
- public int print(Graphics pg, PageFormat pf, int pi)
- throws PrinterException
- {
- pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
+ if (y < 0)
+ {
+ y = 0;
+ }
- int pwidth = (int) pf.getImageableWidth();
- int pheight = (int) pf.getImageableHeight();
+ if (x < 0)
+ {
+ x = 0;
+ }
- if (av.getWrapAlignment())
- {
- return printWrappedAlignment(pg, pwidth, pheight, pi);
+ hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
+ vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
}
- 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());
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void adjustmentValueChanged(AdjustmentEvent evt)
+ {
- ////////////////////////////////////
- /// How many sequences and residues can we fit on a printable page?
- int totalRes = (pwidth - idWidth) / av.getCharWidth();
+ int oldX = av.getStartRes();
+ int oldY = av.getStartSeq();
- int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) -
- 1;
+ if (evt.getSource() == hscroll)
+ {
+ int x = hscroll.getValue();
+ av.setStartRes(x);
+ av.setEndRes((x +
+ (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
+ }
- int pagesWide = (av.getAlignment().getWidth() / totalRes) + 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()));
+ }
+ }
- /////////////////////////////
- /// Only print these sequences and residues on this page
- int startRes;
+ if (overviewPanel != null)
+ {
+ overviewPanel.setBoxPosition();
+ }
- /////////////////////////////
- /// Only print these sequences and residues on this page
- int endRes;
+ int xShift = av.getStartRes() - oldX;
+ int yShift = av.getStartSeq() - oldY;
- /////////////////////////////
- /// Only print these sequences and residues on this page
- int startSeq;
+ 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);
- /////////////////////////////
- /// Only print these sequences and residues on this page
- int endSeq;
- startRes = (pi % pagesWide) * totalRes;
- endRes = (startRes + totalRes) - 1;
+ scalePanel.repaint();
- 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())
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g DOCUMENT ME!
+ */
+ public void paintComponent(Graphics g)
{
- endSeq = av.getAlignment().getHeight();
- }
+ 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;
-
- if (pi >= (pagesWide * pagesHigh))
+ /**
+ * 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
{
- return Printable.NO_SUCH_PAGE;
- }
+ pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
- //draw Scale
- pg.translate(idWidth, 0);
- scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
- pg.translate( -idWidth, scaleHeight);
+ int pwidth = (int) pf.getImageableWidth();
+ int pheight = (int) pf.getImageableHeight();
- ////////////////
- // Draw the ids
- Color currentColor = null;
- Color currentTextColor = null;
+ if (av.getWrapAlignment())
+ {
+ return printWrappedAlignment(pg, pwidth, pheight, pi);
+ }
+ else
+ {
+ return printUnwrapped(pg, pwidth, pheight, pi);
+ }
+ }
- for (int i = startSeq; i < endSeq; i++)
+ /**
+ * 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
{
- 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;
- }
+ int idWidth = calculateIdWidth().width + 4;
+ FontMetrics fm = getFontMetrics(av.getFont());
+ int scaleHeight = av.charHeight + fm.getDescent();
- pg.setColor(currentColor);
- pg.fillRect(0,
- jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,
- av.getCharHeight()), idWidth, av.getCharHeight());
+ pg.setColor(Color.white);
+ pg.fillRect(0, 0, pwidth, pheight);
+ pg.setFont(av.getFont());
- pg.setColor(currentTextColor);
+ ////////////////////////////////////
+ /// How many sequences and residues can we fit on a printable page?
+ int totalRes = (pwidth - idWidth) / av.getCharWidth();
- String string = av.getAlignment().getSequenceAt(i).getName();
+ int totalSeq = (int) ((pheight - scaleHeight) / av.getCharHeight()) -
+ 1;
- if (av.getShowFullId())
- {
- string = av.getAlignment().getSequenceAt(i).getDisplayId();
- }
+ int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
- pg.drawString(string, 0,
- (jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,
- av.getCharHeight()) + av.getCharHeight()) -
- (av.getCharHeight() / 5));
- }
+ /////////////////////////////
+ /// Only print these sequences and residues on this page
+ int startRes;
- // draw main sequence panel
- pg.translate(idWidth, 0);
- seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,
- startRes, startSeq, 0);
+ /////////////////////////////
+ /// Only print these sequences and residues on this page
+ int endRes;
- 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 startSeq;
- return Printable.PAGE_EXISTS;
- }
+ /////////////////////////////
+ /// Only print these sequences and residues on this page
+ int endSeq;
+ startRes = (pi % pagesWide) * totalRes;
+ endRes = (startRes + totalRes) - 1;
- public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
- int pi)
- throws PrinterException
- {
- int idWidth = calculateIdWidth().width + 4;
+ if (endRes > (av.getAlignment().getWidth() - 1))
+ {
+ endRes = av.getAlignment().getWidth() - 1;
+ }
- int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
- idWidth);
- int totalHeight = totalHeight = (av.alignment.getHeight() + 2) *
- ( (av.alignment.getWidth() / resWidth) +
- 1) * av.charHeight;
+ startSeq = (pi / pagesWide) * totalSeq;
+ endSeq = startSeq + totalSeq;
- pg.setColor(Color.white);
- pg.fillRect(0, 0, pwidth, pheight);
- pg.setFont(av.getFont());
+ if (endSeq > av.getAlignment().getHeight())
+ {
+ endSeq = av.getAlignment().getHeight();
+ }
+
+ int pagesHigh = ((av.alignment.getHeight() / totalSeq) + 1) * pheight;
- ////////////////
- // Draw the ids
- pg.setColor(Color.black);
+ if (av.showAnnotation)
+ {
+ pagesHigh += annotationPanel.getHeight();
+ }
- pg.translate(0, -pi * pheight);
+ pagesHigh /= pheight;
- pg.setClip(0, pi * pheight, pwidth, pheight);
+ if (pi >= (pagesWide * pagesHigh))
+ {
+ return Printable.NO_SUCH_PAGE;
+ }
- int ypos = 2 * av.charHeight;
+ //draw Scale
+ pg.translate(idWidth, 0);
+ scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
+ pg.translate(-idWidth, scaleHeight);
- do
- {
- for (int i = 0; i < av.alignment.getHeight(); i++)
- {
- SequenceI s = av.alignment.getSequenceAt(i);
- String string = s.getName();
+ ////////////////
+ // Draw the ids
+ Color currentColor = null;
+ Color currentTextColor = null;
- if (av.getShowFullId())
+ for (int i = startSeq; i < endSeq; i++)
{
- 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);
- pg.translate(idWidth, 0);
+ /**
+ * 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;
- seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
+ int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
+ idWidth);
+ int totalHeight = totalHeight = (av.alignment.getHeight() + 2) * ((av.alignment.getWidth() / resWidth) +
+ 1) * av.charHeight;
- if ( (pi * pheight) < totalHeight)
- {
- return Printable.PAGE_EXISTS;
- }
- else
- {
- return Printable.NO_SUCH_PAGE;
- }
- }
+ pg.setColor(Color.white);
+ pg.fillRect(0, 0, pwidth, pheight);
+ pg.setFont(av.getFont());
- public void makeEPS()
- {
- int height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *
- av.chunkHeight;
- int width = seqPanel.getWidth() + idPanel.getWidth();
+ ////////////////
+ // Draw the ids
+ pg.setColor(Color.black);
- if (!av.getWrapAlignment())
- {
- height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
- width = idPanel.getWidth() +
- (av.alignment.getWidth() * av.charWidth);
- }
+ pg.translate(0, -pi * pheight);
- if (av.getShowAnnotation())
- {
- height += annotationPanel.getPreferredSize().height;
- }
+ pg.setClip(0, pi * pheight, pwidth, pheight);
- 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;
- }
+ int ypos = 2 * av.charHeight;
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- chooser.getSelectedFile().getParent());
+ 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);
- FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
- EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width,
- height);
+ pg.translate(idWidth, 0);
- if (av.getWrapAlignment())
- {
- printWrappedAlignment(pg, width, height, 0);
- }
- else
- {
- printUnwrapped(pg, width, height, 0);
- }
+ seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
- pg.flush();
- pg.close();
+ if ((pi * pheight) < totalHeight)
+ {
+ return Printable.PAGE_EXISTS;
+ }
+ else
+ {
+ return Printable.NO_SUCH_PAGE;
+ }
}
- catch (Exception ex)
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void makeEPS(File epsFile)
{
- ex.printStackTrace();
- }
- }
+ 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());
+ }
- public void makePNG()
- {
- int height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *
- av.chunkHeight;
- int width = seqPanel.getWidth() + idPanel.getWidth();
+ int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
+ int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
- if (!av.getWrapAlignment())
- {
- height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
- width = idPanel.getWidth() +
- (av.alignment.getWidth() * av.charWidth);
+ if (av.getWrapAlignment())
+ {
+ height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *
+ av.chunkHeight;
+ width = seqPanel.getWidth() + idPanel.getWidth();
+
+ }
+
+
+ if (av.getShowAnnotation())
+ {
+ height += annotationPanel.getPreferredSize().height;
+ }
+
+ 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();
+ }
}
- if (av.getShowAnnotation())
+
+ public void makePNGImageMap(File imgMapFile, String imageName)
{
- height += annotationPanel.getPreferredSize().height;
+ ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
+ //////////////////////////////////////////////
+ int idWidth = calculateIdWidth().width + 4;
+ FontMetrics fm = getFontMetrics(av.getFont());
+ int scaleHeight = av.charHeight + fm.getDescent();
+
+ // Gen image map
+ //////////////////////////////////
+ if(imgMapFile!=null)
+ {
+ try
+ {
+ PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
+ out.println(jalview.io.HTMLOutput.getImageMapHTML());
+ out.println("
"
+ +"