X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=6cd18babd45a22cced793f483472aa676e439e52;hb=d0b7395c10aec7c5da5a5662fc69783ec78fae8d;hp=1a48af6fbe1471e03fd96d4fbbb6dc0825674cb5;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 1a48af6..6cd18ba 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,6 +1,6 @@
/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,29 +18,34 @@
*/
package jalview.gui;
+import java.beans.*;
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.*;
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
public class AlignmentPanel
extends GAlignmentPanel implements AdjustmentListener, Printable
{
- AlignViewport av;
+ public AlignViewport av;
OverviewPanel overviewPanel;
SeqPanel seqPanel;
IdPanel idPanel;
IdwidthAdjuster idwidthAdjuster;
+
+ /** DOCUMENT ME!! */
public AlignFrame alignFrame;
ScalePanel scalePanel;
AnnotationPanel annotationPanel;
@@ -51,6 +56,12 @@ public class AlignmentPanel
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;
@@ -67,49 +78,56 @@ public class AlignmentPanel
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);
+ setAnnotationVisible(av.getShowAnnotation());
+
hscroll.addAdjustmentListener(this);
vscroll.addAdjustmentListener(this);
- setFocusable(true);
- addKeyListener(new KeyAdapter()
+ final AlignmentPanel ap = this;
+ av.addPropertyChangeListener(new PropertyChangeListener()
{
- public void keyPressed(KeyEvent evt)
+ public void propertyChange(PropertyChangeEvent evt)
{
- switch (evt.getKeyCode())
+ if (evt.getPropertyName().equals("alignment"))
{
- case 27: // escape key
- av.setSelectionGroup(null);
- repaint();
+ PaintRefresher.Refresh(ap,
+ av.getSequenceSetId(),
+ true,
+ true);
+ alignmentChanged();
+ }
+ }
+ });
- break;
+ fontChanged();
- case KeyEvent.VK_DOWN:
- alignFrame.moveSelectedSequences(false);
+ }
- break;
+ public void alignmentChanged()
+ {
+ av.alignmentChanged(this);
- case KeyEvent.VK_UP:
- alignFrame.moveSelectedSequences(true);
+ if (overviewPanel != null)
+ {
+ overviewPanel.updateOverviewImage();
+ }
- break;
- }
- }
- });
+ alignFrame.updateEditMenuBar();
+
+ repaint();
}
+ /**
+ * DOCUMENT ME!
+ */
public void fontChanged()
{
// set idCanvas bufferedImage to null
@@ -122,27 +140,34 @@ public class AlignmentPanel
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();
}
- Dimension calculateIdWidth()
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Dimension calculateIdWidth()
{
- Graphics g = this.getGraphics();
+ Container c = new Container();
- if (g == null)
- {
- javax.swing.JFrame f = new javax.swing.JFrame();
- f.addNotify();
- g = f.getGraphics();
- }
+ FontMetrics fm = c.getFontMetrics(
+ new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
- FontMetrics fm = g.getFontMetrics(av.font);
AlignmentI al = av.getAlignment();
int i = 0;
@@ -153,14 +178,7 @@ public class AlignmentPanel
{
SequenceI s = al.getSequenceAt(i);
- if (av.getShowFullId())
- {
- id = s.getDisplayId();
- }
- else
- {
- id = s.getName();
- }
+ id = s.getDisplayId(av.getShowJVSuffix());
if (fm.stringWidth(id) > idWidth)
{
@@ -175,7 +193,7 @@ public class AlignmentPanel
if (al.getAlignmentAnnotation() != null)
{
- fm = g.getFontMetrics(alabels.getFont());
+ fm = c.getFontMetrics(alabels.getFont());
while (i < al.getAlignmentAnnotation().length)
{
@@ -193,76 +211,138 @@ public class AlignmentPanel
return new Dimension(idWidth, 12);
}
- public void highlightSearchResults(int[] results)
+ /**
+ * 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 = av.alignment.getSequenceAt(results[0]);
- int start = seq.findIndex(results[1]) - 1;
- int end = seq.findIndex(results[2]) - 1;
+ 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.getStartRes() > start) || (av.getEndRes() < end) ||
- ( (av.getStartSeq() > results[0]) ||
- (av.getEndSeq() < results[0])))
+ if (!av.wrapAlignment)
+ {
+ if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||
+ ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
+ {
+ setScrollValues(start, seqIndex);
+ }
+ }
+ else
{
- setScrollValues(start, results[0]);
+ 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)
{
- annotationSpaceFillerHolder.setVisible(b);
- annotationScroller.setVisible(b);
+ if (!av.wrapAlignment)
+ {
+ annotationSpaceFillerHolder.setVisible(b);
+ annotationScroller.setVisible(b);
+ }
+ repaint();
}
- public void setWrapAlignment(boolean wrap)
+ public void adjustAnnotationHeight()
{
- scalePanelHolder.setVisible(!wrap);
- hscroll.setVisible(!wrap);
- idwidthAdjuster.setVisible(!wrap);
+ if (alignFrame.getHeight() == 0)
+ {
+ System.out.println("NEEDS FIXING");
+ }
- av.setShowAnnotation(!wrap);
- annotationScroller.setVisible(!wrap);
- annotationSpaceFillerHolder.setVisible(!wrap);
- idSpaceFillerPanel1.setVisible(!wrap);
+ int height = annotationPanel.adjustPanelHeight() +
+ hscroll.getPreferredSize().height;
+
+ if (height > alignFrame.getHeight() / 2)
+ {
+ height = alignFrame.getHeight() / 2;
+ }
+
+ hscroll.addNotify();
+
+ annotationScroller.setPreferredSize(
+ new Dimension(annotationScroller.getWidth(),
+ height + hscroll.getHeight()));
+
+
+ annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+ annotationSpaceFillerHolder.getWidth(),
+ height));
repaint();
}
- public void setColourScheme()
+ /**
+ * DOCUMENT ME!
+ *
+ * @param wrap DOCUMENT ME!
+ */
+ public void setWrapAlignment(boolean wrap)
{
- ColourSchemeI cs = av.getGlobalColourScheme();
+ av.startSeq = 0;
+ scalePanelHolder.setVisible(!wrap);
+ hscroll.setVisible(!wrap);
+ idwidthAdjuster.setVisible(!wrap);
- if (av.getConservationSelected())
+ if (wrap)
{
- 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);
+ annotationScroller.setVisible(false);
+ annotationSpaceFillerHolder.setVisible(false);
+ }
+ else if (av.showAnnotation)
+ {
+ annotationScroller.setVisible(true);
+ annotationSpaceFillerHolder.setVisible(true);
}
+ idSpaceFillerPanel1.setVisible(!wrap);
+
repaint();
}
@@ -295,9 +375,16 @@ public class AlignmentPanel
return true;
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param right DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
public boolean scrollRight(boolean right)
{
- if (right)
+ if (!right)
{
if (hscroll.getValue() < 1)
{
@@ -323,32 +410,46 @@ public class AlignmentPanel
return true;
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param x DOCUMENT ME!
+ * @param y DOCUMENT ME!
+ */
public void setScrollValues(int x, int y)
{
- av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -
- 1);
+
+ 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 > av.alignment.getWidth())
+ if (hextent > width)
{
- hextent = av.alignment.getWidth();
+ hextent = width;
}
- if (vextent > av.alignment.getHeight())
+ if (vextent > height)
{
- vextent = av.alignment.getHeight();
+ vextent = height;
}
- if ( (hextent + x) > av.getAlignment().getWidth())
+ if ( (hextent + x) > width)
{
- x = av.getAlignment().getWidth() - hextent;
+ x = width - hextent;
}
- if ( (vextent + y) > av.getAlignment().getHeight())
+ if ( (vextent + y) > height)
{
- y = av.getAlignment().getHeight() - vextent;
+ y = height - vextent;
}
if (y < 0)
@@ -361,12 +462,18 @@ public class AlignmentPanel
x = 0;
}
- hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
- vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
+ 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();
@@ -384,10 +491,26 @@ public class AlignmentPanel
if (av.getWrapAlignment())
{
- int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
- seqCanvas.getWidth());
- av.setStartRes(vscroll.getValue() * rowSize);
- av.setEndRes( (vscroll.getValue() + 1) * rowSize);
+ 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
{
@@ -402,25 +525,62 @@ public class AlignmentPanel
overviewPanel.setBoxPosition();
}
+ int scrollX = av.startRes - oldX;
+ int scrollY = av.startSeq - oldY;
+
if (av.getWrapAlignment() || !fastPaint)
{
repaint();
}
else
{
- idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
- seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
- av.getStartSeq() - oldY);
+ // 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;
+ }
- scalePanel.repaint();
+ if (scrollX != 0 || scrollY != 0)
+ {
+ idPanel.idCanvas.fastPaint(scrollY);
+ seqPanel.seqCanvas.fastPaint(scrollX,
+ scrollY);
+ scalePanel.repaint();
- if (av.getShowAnnotation())
+ if (av.getShowAnnotation())
+ {
+ annotationPanel.fastPaint(scrollX);
+ }
+ }
+ }
+ }
+
+ public void paintAlignment(boolean updateOverview)
+ {
+ repaint();
+
+ if(updateOverview)
+ {
+ jalview.structure.StructureSelectionManager.getStructureSelectionManager()
+ .sequenceColoursChanged(this);
+
+ if (overviewPanel != null)
{
- annotationPanel.fastPaint(av.getStartRes() - oldX);
+ overviewPanel.updateOverviewImage();
}
}
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g DOCUMENT ME!
+ */
public void paintComponent(Graphics g)
{
invalidate();
@@ -432,11 +592,25 @@ public class AlignmentPanel
if (av.getWrapAlignment())
{
- int max = av.alignment.getWidth() /
- seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
- vscroll.setMaximum(max);
- vscroll.setUnitIncrement(1);
- vscroll.setVisibleAmount(1);
+ 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
{
@@ -444,6 +618,17 @@ public class AlignmentPanel
}
}
+ /**
+ * 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
{
@@ -462,10 +647,22 @@ public class AlignmentPanel
}
}
+ /**
+ * 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;
+ int idWidth = getVisibleIdWidth();
FontMetrics fm = getFontMetrics(av.getFont());
int scaleHeight = av.charHeight + fm.getDescent();
@@ -517,7 +714,7 @@ public class AlignmentPanel
if (av.showAnnotation)
{
- pagesHigh += annotationPanel.getHeight();
+ pagesHigh += annotationPanel.adjustPanelHeight() + 3;
}
pagesHigh /= pheight;
@@ -537,51 +734,56 @@ public class AlignmentPanel
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().sequences.contains(
- av.getAlignment().getSequenceAt(i)))
+ av.getSelectionGroup().getSequences(null).contains(seq))
{
currentColor = Color.gray;
currentTextColor = Color.black;
}
else
{
- currentColor = av.getAlignment().getSequenceAt(i).getColor();
+ currentColor = av.getSequenceColour(seq);
currentTextColor = Color.black;
}
pg.setColor(currentColor);
- pg.fillRect(0,
- jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,
- av.getCharHeight()), idWidth, av.getCharHeight());
+ pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
+ av.getCharHeight());
pg.setColor(currentTextColor);
- String string = av.getAlignment().getSequenceAt(i).getName();
-
- if (av.getShowFullId())
+ int xPos = 0;
+ if (av.rightAlignIds)
{
- string = av.getAlignment().getSequenceAt(i).getDisplayId();
+ fm = pg.getFontMetrics();
+ xPos = idWidth - fm.stringWidth(
+ seq.getDisplayId(av.getShowJVSuffix())
+ ) - 4;
}
- pg.drawString(string, 0,
- (jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,
- av.getCharHeight()) + av.getCharHeight()) -
+ 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,
- startRes, startSeq, 0);
+ seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
{
- pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight);
- alabels.drawComponent( (Graphics2D) pg);
- pg.translate(idWidth, 0);
+ 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);
}
@@ -589,17 +791,53 @@ public class AlignmentPanel
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 idWidth = calculateIdWidth().width + 4;
+
+ 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 = totalHeight = (av.alignment.getHeight() + 2) *
- ( (av.alignment.getWidth() / resWidth) +
- 1) * av.charHeight;
+
+ int totalHeight = cHeight * (maxwidth / resWidth + 1);
pg.setColor(Color.white);
pg.fillRect(0, 0, pwidth, pheight);
@@ -613,26 +851,39 @@ public class AlignmentPanel
pg.setClip(0, pi * pheight, pwidth, pheight);
- int ypos = 2 * av.charHeight;
+ 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.getName();
-
- if (av.getShowFullId())
+ String string = s.getDisplayId(av.getShowJVSuffix());
+ int xPos = 0;
+ if (av.rightAlignIds)
{
- string = s.getDisplayId();
+ FontMetrics fm = pg.getFontMetrics();
+ xPos = idWidth - fm.stringWidth(string) - 4;
}
-
- pg.drawString(string, 0,
- (AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +
- av.charHeight) - (av.charHeight / 5));
+ 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 += ( (av.alignment.getHeight() + 2) * av.charHeight);
+ ypos += cHeight;
}
while (ypos < totalHeight);
@@ -643,6 +894,7 @@ public class AlignmentPanel
if ( (pi * pheight) < totalHeight)
{
return Printable.PAGE_EXISTS;
+
}
else
{
@@ -650,172 +902,304 @@ public class AlignmentPanel
}
}
- public void makeEPS()
+ int getVisibleIdWidth()
{
- int height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *
- av.chunkHeight;
- int width = seqPanel.getWidth() + idPanel.getWidth();
+ return
+ idPanel.getWidth() > 0 ? idPanel.getWidth() :
+ calculateIdWidth().width + 4;
+ }
- if (!av.getWrapAlignment())
+ void makeAlignmentImage(int type, File file)
+ {
+ int maxwidth = av.alignment.getWidth();
+ if (av.hasHiddenColumns)
{
- height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
- width = idPanel.getWidth() +
- (av.alignment.getWidth() * av.charWidth);
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
}
- if (av.getShowAnnotation())
- {
- height += annotationPanel.getPreferredSize().height;
- }
+ int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
+ int width = getVisibleIdWidth() + (maxwidth * av.charWidth);
- try
+ if (av.getWrapAlignment())
{
- 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)
+ height = getWrappedHeight();
+ if (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true"))
{
- 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);
+ width = alignFrame.getWidth()
+ - vscroll.getPreferredSize().width
+ - alignFrame.getInsets().left
+ - alignFrame.getInsets().right;
}
else
{
- printUnwrapped(pg, width, height, 0);
+ width = seqPanel.getWidth() + getVisibleIdWidth();
}
- 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())
+ else if (av.getShowAnnotation())
{
- height += annotationPanel.getPreferredSize().height;
+ height += annotationPanel.adjustPanelHeight() + 3;
}
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)
+ jalview.util.ImageMaker im;
+ if (type == jalview.util.ImageMaker.PNG)
{
- return;
+ 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());
}
-
- 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);
+ if (im.getGraphics() != null)
+ {
+ printWrappedAlignment(im.getGraphics(), width, height, 0);
+ im.writeImage();
+ }
}
else
{
- printUnwrapped(png, width, height, 0);
+ 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();
- ImageIO.write(bi, "png", out);
- out.close();
}
catch (Exception ex)
{
ex.printStackTrace();
}
}
-}
-class Preview
- extends JFrame
-{
- public Preview(Image image)
+ /**
+ * DOCUMENT ME!
+ */
+ public void makeEPS(File epsFile)
{
- setResizable(true);
- setSize(image.getWidth(this), image.getHeight(this));
- setVisible(true);
- getContentPane().setLayout(new BorderLayout());
- getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);
- validate();
- repaint();
+ makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
}
-}
-class PreviewPanel
- extends JPanel
-{
- Image image;
+ /**
+ * DOCUMENT ME!
+ */
+ public void makePNG(File pngFile)
+ {
+ makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
+ }
- public PreviewPanel(Image image)
+ public void makePNGImageMap(File imgMapFile, String imageName)
{
- this.image = image;
+ ///////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("
"
+ + "