X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=43fb5fac17366c74ad8740bb2dec6d27385d3d0a;hb=32ce9ddb7ce1a68add53dd81785ae428ca136a83;hp=1a48af6fbe1471e03fd96d4fbbb6dc0825674cb5;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 1a48af6..43fb5fa 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -18,29 +18,37 @@
*/
package jalview.gui;
-import java.io.*;
-import javax.imageio.*;
+import jalview.datamodel.*;
+
+import jalview.jbgui.*;
+
+import jalview.schemes.*;
import java.awt.*;
import java.awt.event.*;
-import java.awt.image.*;
import java.awt.print.*;
+
+import java.io.*;
+
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;
+ public AlignViewport av;
OverviewPanel overviewPanel;
SeqPanel seqPanel;
IdPanel idPanel;
IdwidthAdjuster idwidthAdjuster;
+
+ /** DOCUMENT ME!! */
public AlignFrame alignFrame;
ScalePanel scalePanel;
AnnotationPanel annotationPanel;
@@ -51,6 +59,12 @@ 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;
@@ -80,11 +94,17 @@ public class AlignmentPanel
setScrollValues(0, 0);
+ annotationPanel.adjustPanelHeight();
+ annotationSpaceFillerHolder.setPreferredSize(annotationPanel.
+ getPreferredSize());
+ annotationScroller.setPreferredSize(annotationPanel.
+ getPreferredSize());
+ setAnnotationVisible(av.getShowAnnotation());
+
hscroll.addAdjustmentListener(this);
vscroll.addAdjustmentListener(this);
- setFocusable(true);
- addKeyListener(new KeyAdapter()
+ af.addKeyListener(new KeyAdapter()
{
public void keyPressed(KeyEvent evt)
{
@@ -105,11 +125,26 @@ public class AlignmentPanel
alignFrame.moveSelectedSequences(true);
break;
+
+ case KeyEvent.VK_BACK_SPACE:
+ case KeyEvent.VK_DELETE:
+ alignFrame.cut_actionPerformed(null);
+ break;
+
+ case KeyEvent.VK_P:
+ seqPanel.seqCanvas.increaseAARatio();
+ break;
+ case KeyEvent.VK_L:
+ seqPanel.seqCanvas.decreaseAARation();
+ break;
}
}
});
}
+ /**
+ * DOCUMENT ME!
+ */
public void fontChanged()
{
// set idCanvas bufferedImage to null
@@ -122,27 +157,43 @@ 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 (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();
+
repaint();
}
- Dimension calculateIdWidth()
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Dimension calculateIdWidth()
{
- Graphics g = this.getGraphics();
-
- if (g == null)
- {
- javax.swing.JFrame f = new javax.swing.JFrame();
- f.addNotify();
- g = f.getGraphics();
- }
+ Container c = new Container();
- FontMetrics fm = g.getFontMetrics(av.font);
+ FontMetrics fm = c.getFontMetrics(av.font);
AlignmentI al = av.getAlignment();
int i = 0;
@@ -153,14 +204,7 @@ 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 +219,7 @@ public class AlignmentPanel
if (al.getAlignmentAnnotation() != null)
{
- fm = g.getFontMetrics(alabels.getFont());
+ fm = c.getFontMetrics(alabels.getFont());
while (i < al.getAlignmentAnnotation().length)
{
@@ -193,6 +237,11 @@ public class AlignmentPanel
return new Dimension(idWidth, 12);
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param results DOCUMENT ME!
+ */
public void highlightSearchResults(int[] results)
{
seqPanel.seqCanvas.highlightSearchResults(results);
@@ -213,56 +262,66 @@ public class AlignmentPanel
}
}
+ /**
+ * 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();
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param wrap DOCUMENT ME!
+ */
public void setWrapAlignment(boolean wrap)
{
+ av.startSeq = 0;
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())
+ 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();
}
@@ -295,6 +354,13 @@ public class AlignmentPanel
return true;
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param right DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
public boolean scrollRight(boolean right)
{
if (right)
@@ -323,6 +389,12 @@ 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())) -
@@ -365,8 +437,14 @@ public class AlignmentPanel
vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
public void adjustmentValueChanged(AdjustmentEvent evt)
{
+
int oldX = av.getStartRes();
int oldY = av.getStartSeq();
@@ -402,25 +480,37 @@ public class AlignmentPanel
overviewPanel.setBoxPosition();
}
- if (av.getWrapAlignment() || !fastPaint)
+ int xShift = av.getStartRes() - oldX;
+ int yShift = av.getStartSeq() - oldY;
+
+ 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(av.getStartSeq() - oldY);
- seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
- av.getStartSeq() - oldY);
+ idPanel.idCanvas.fastPaint(yShift);
+ seqPanel.seqCanvas.fastPaint(xShift, yShift);
scalePanel.repaint();
if (av.getShowAnnotation())
{
- annotationPanel.fastPaint(av.getStartRes() - oldX);
+ annotationPanel.fastPaint(xShift);
}
}
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g DOCUMENT ME!
+ */
public void paintComponent(Graphics g)
{
invalidate();
@@ -442,8 +532,26 @@ public class AlignmentPanel
{
setScrollValues(av.getStartRes(), av.getStartSeq());
}
+
+
+ if( this.getVisibleRect().getBounds() == g.getClipBounds() )
+ {
+ if (overviewPanel != null)
+ overviewPanel.updateOverviewImage();
+ }
}
+ /**
+ * 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
{
@@ -462,6 +570,18 @@ 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
{
@@ -517,7 +637,7 @@ public class AlignmentPanel
if (av.showAnnotation)
{
- pagesHigh += annotationPanel.getHeight();
+ pagesHigh += annotationPanel.adjustPanelHeight() + 3;
}
pagesHigh /= pheight;
@@ -553,22 +673,16 @@ public class AlignmentPanel
}
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())
- {
- string = av.getAlignment().getSequenceAt(i).getDisplayId();
- }
+ String string = av.getAlignment().getSequenceAt(i).getDisplayId
+ ( av.getShowJVSuffix());
pg.drawString(string, 0,
- (jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,
- av.getCharHeight()) + av.getCharHeight()) -
+ ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
(av.getCharHeight() / 5));
}
@@ -579,8 +693,8 @@ public class AlignmentPanel
if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
{
- pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight);
- alabels.drawComponent( (Graphics2D) pg);
+ pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight + 3);
+ alabels.drawComponent( (Graphics2D) pg, idWidth);
pg.translate(idWidth, 0);
annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +
1);
@@ -589,17 +703,45 @@ 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 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 = calculateIdWidth().width + 4;
int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
idWidth);
- int totalHeight = totalHeight = (av.alignment.getHeight() + 2) *
- ( (av.alignment.getWidth() / resWidth) +
- 1) * av.charHeight;
+
+ int totalHeight = cHeight * (av.alignment.getWidth() / resWidth + 1);
pg.setColor(Color.white);
pg.fillRect(0, 0, pwidth, pheight);
@@ -613,26 +755,37 @@ public class AlignmentPanel
pg.setClip(0, pi * pheight, pwidth, pheight);
- int ypos = 2 * av.charHeight;
+ int ypos = hgap;
+ Font italic = new Font(av.getFont().getName(), Font.ITALIC,
+ av.getFont().getSize());
+ pg.setFont(italic);
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();
- }
+ String string = s.getDisplayId( av.getShowJVSuffix());
pg.drawString(string, 0,
- (AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +
- av.charHeight) - (av.charHeight / 5));
+ ( (i * av.charHeight) + ypos + av.charHeight) -
+ (av.charHeight / 5));
+ }
+ if (labels != null)
+ {
+ pg.translate(0,
+ ypos +
+ (av.getAlignment().getHeight() * av.charHeight));
+
+ pg.setFont(av.getFont());
+ labels.drawComponent(pg, idWidth);
+ pg.setFont(italic);
+ pg.translate(0,
+ -ypos -
+ (av.getAlignment().getHeight() * av.charHeight));
}
- ypos += ( (av.alignment.getHeight() + 2) * av.charHeight);
+ ypos += cHeight;
}
while (ypos < totalHeight);
@@ -643,6 +796,7 @@ public class AlignmentPanel
if ( (pi * pheight) < totalHeight)
{
return Printable.PAGE_EXISTS;
+
}
else
{
@@ -650,172 +804,237 @@ public class AlignmentPanel
}
}
- public void makeEPS()
+ void makeAlignmentImage(int type, File file)
{
- 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())
+ if (av.getWrapAlignment())
{
- height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
- width = idPanel.getWidth() +
- (av.alignment.getWidth() * av.charWidth);
+ height = getWrappedHeight();
+ width = seqPanel.getWidth() + idPanel.getWidth();
}
-
- if (av.getShowAnnotation())
+ else if (av.getShowAnnotation())
{
- height += annotationPanel.getPreferredSize().height;
+ height += annotationPanel.adjustPanelHeight() + 3;
}
+ jalview.util.ImageMaker im;
+ if(type==jalview.util.ImageMaker.PNG)
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.PNG,
+ "Create PNG image from alignment",
+ width, height, file, null);
+ else
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.EPS,
+ "Create EPS file from alignment",
+ width, height, file, alignFrame.getTitle() );
+
try
{
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty(
- "LAST_DIRECTORY"), new String[]
- {"eps"},
- new String[]
- {"Encapsulated Postscript"},
- "Encapsulated Postscript");
- chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Create EPS file from alignment");
- chooser.setToolTipText("Save");
-
- int value = chooser.showSaveDialog(this);
-
- if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
- {
- return;
- }
-
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- chooser.getSelectedFile().getParent());
-
- FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
- EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width,
- height);
-
if (av.getWrapAlignment())
{
- printWrappedAlignment(pg, width, height, 0);
+ if(im.getGraphics()!=null)
+ printWrappedAlignment(im.getGraphics(), width, height, 0);
}
else
{
- printUnwrapped(pg, width, height, 0);
+ if(im.getGraphics()!=null)
+ printUnwrapped(im.getGraphics(), width, height, 0);
}
- pg.flush();
- pg.close();
+ im.writeImage();
+ }
+ catch (OutOfMemoryError err)
+ {
+ System.out.println("########################\n"
+ + "OUT OF MEMORY " + file + "\n"
+ + "########################");
+
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Out of Memory Creating Image!!"
+ +
+ "\nSee help files for increasing Java Virtual Machine memory."
+ , "Out of memory",
+ JOptionPane.WARNING_MESSAGE);
+ System.out.println("Create IMAGE: " + err);
+ System.gc();
+
}
catch (Exception ex)
{
ex.printStackTrace();
}
}
+ /**
+ * DOCUMENT ME!
+ */
+ public void makeEPS(File epsFile)
+ {
+ makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
+ }
- public void makePNG()
+ /**
+ * DOCUMENT ME!
+ */
+ public void makePNG(File pngFile)
{
- int height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *
- av.chunkHeight;
- int width = seqPanel.getWidth() + idPanel.getWidth();
+ makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
+ }
- if (!av.getWrapAlignment())
- {
- height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
- width = idPanel.getWidth() +
- (av.alignment.getWidth() * av.charWidth);
- }
+ public void makePNGImageMap(File imgMapFile, String imageName)
+ {
+ ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
+ //////////////////////////////////////////////
+ int idWidth = calculateIdWidth().width + 4;
+ FontMetrics fm = getFontMetrics(av.getFont());
+ int scaleHeight = av.charHeight + fm.getDescent();
- if (av.getShowAnnotation())
+ // Gen image map
+ //////////////////////////////////
+ if (imgMapFile != null)
{
- height += annotationPanel.getPreferredSize().height;
- }
+ try
+ {
+ PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
+ out.println(jalview.io.HTMLOutput.getImageMapHTML());
+ out.println(""
+ + "