*/\r
package jalview.gui;\r
\r
-import java.io.*;\r
-import javax.imageio.*;\r
+import jalview.datamodel.*;\r
+\r
+import jalview.jbgui.*;\r
+\r
+import jalview.schemes.*;\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
-import java.awt.image.*;\r
import java.awt.print.*;\r
+\r
+import java.io.*;\r
+\r
import javax.swing.*;\r
\r
-import org.jibble.epsgraphics.*;\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
-import jalview.jbgui.*;\r
-import jalview.schemes.*;\r
\r
-public class AlignmentPanel\r
- extends GAlignmentPanel implements AdjustmentListener, Printable\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class AlignmentPanel extends GAlignmentPanel\r
+ implements AdjustmentListener, Printable\r
{\r
- AlignViewport av;\r
+ public AlignViewport av;\r
OverviewPanel overviewPanel;\r
SeqPanel seqPanel;\r
IdPanel idPanel;\r
IdwidthAdjuster idwidthAdjuster;\r
+\r
+ /** DOCUMENT ME!! */\r
public AlignFrame alignFrame;\r
ScalePanel scalePanel;\r
AnnotationPanel annotationPanel;\r
AnnotationLabels alabels;\r
\r
// this value is set false when selection area being dragged\r
- boolean fastPaint = false;\r
+ boolean fastPaint = true;\r
int hextent = 0;\r
int vextent = 0;\r
\r
+ /**\r
+ * Creates a new AlignmentPanel object.\r
+ *\r
+ * @param af DOCUMENT ME!\r
+ * @param av DOCUMENT ME!\r
+ */\r
public AlignmentPanel(AlignFrame af, final AlignViewport av)\r
{\r
alignFrame = af;\r
annotationPanel = new AnnotationPanel(this);\r
alabels = new AnnotationLabels(this);\r
\r
- annotationSpaceFillerHolder.setPreferredSize(annotationPanel.\r
- getPreferredSize());\r
- annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());\r
+\r
annotationScroller.setViewportView(annotationPanel);\r
annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);\r
\r
\r
setScrollValues(0, 0);\r
\r
+ annotationPanel.adjustPanelHeight();\r
+ annotationSpaceFillerHolder.setPreferredSize(annotationPanel.\r
+ getPreferredSize());\r
+ annotationScroller.setPreferredSize(annotationPanel.\r
+ getPreferredSize());\r
+ setAnnotationVisible(av.getShowAnnotation());\r
+\r
hscroll.addAdjustmentListener(this);\r
vscroll.addAdjustmentListener(this);\r
\r
- setFocusable(true);\r
- addKeyListener(new KeyAdapter()\r
+ af.addKeyListener(new KeyAdapter()\r
{\r
public void keyPressed(KeyEvent evt)\r
{\r
+ if(av.cursorMode\r
+ && evt.getKeyCode()>=KeyEvent.VK_0\r
+ && evt.getKeyCode()<=KeyEvent.VK_9)\r
+ {\r
+ seqPanel.numberPressed(evt.getKeyChar());\r
+ }\r
+\r
switch (evt.getKeyCode())\r
{\r
case 27: // escape key\r
break;\r
\r
case KeyEvent.VK_DOWN:\r
- alignFrame.moveSelectedSequences(false);\r
-\r
+ if(av.cursorMode)\r
+ {\r
+ seqPanel.moveCursor(0,1);\r
+ }\r
+ else\r
+ alignFrame.moveSelectedSequences(false);\r
break;\r
\r
case KeyEvent.VK_UP:\r
- alignFrame.moveSelectedSequences(true);\r
+ if (av.cursorMode)\r
+ {\r
+ seqPanel.moveCursor(0,-1);\r
+ }\r
+ else\r
+ alignFrame.moveSelectedSequences(true);\r
+ break;\r
+\r
+ case KeyEvent.VK_LEFT:\r
+ if(av.cursorMode)\r
+ {\r
+ seqPanel.moveCursor(-1,0);\r
+ }\r
+ break;\r
\r
+ case KeyEvent.VK_RIGHT:\r
+ if (av.cursorMode)\r
+ {\r
+ seqPanel.moveCursor(1,0);\r
+ }\r
break;\r
+\r
+ case KeyEvent.VK_SPACE:\r
+ if(av.cursorMode)\r
+ {\r
+ seqPanel.insertGapAtCursor(evt.isControlDown() || evt.isShiftDown());\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_DELETE:\r
+ case KeyEvent.VK_BACK_SPACE:\r
+ if(!av.cursorMode)\r
+ {\r
+ alignFrame.cut_actionPerformed(null);\r
+ seqPanel.seqCanvas.repaint();\r
+ }\r
+ else\r
+ seqPanel.deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown());\r
+\r
+ break;\r
+\r
+ case KeyEvent.VK_S:\r
+ if(av.cursorMode)\r
+ {\r
+ seqPanel.setCursorRow();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_C:\r
+ if(av.cursorMode)\r
+ {\r
+ seqPanel.setCursorColumn();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_P:\r
+ if(av.cursorMode)\r
+ {\r
+ seqPanel.setCursorPosition();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_ENTER:\r
+ case KeyEvent.VK_COMMA:\r
+ if(av.cursorMode)\r
+ {\r
+ seqPanel.setCursorRowAndColumn();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_Q:\r
+ if(av.cursorMode)\r
+ {\r
+ seqPanel.setSelectionAreaAtCursor(true);\r
+ }\r
+ break;\r
+ case KeyEvent.VK_M:\r
+ if(av.cursorMode)\r
+ {\r
+ seqPanel.setSelectionAreaAtCursor(false);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_F2:\r
+ av.cursorMode = ! av.cursorMode;\r
+ alignFrame.statusBar.setText("Keyboard editing mode is "+\r
+ (av.cursorMode ? "on" : "off"));\r
+ if(av.cursorMode)\r
+ {\r
+ seqPanel.seqCanvas.cursorX = av.startRes;\r
+ seqPanel.seqCanvas.cursorY = av.startSeq;\r
+ }\r
+ seqPanel.seqCanvas.repaint();\r
+ break;\r
+\r
+ case KeyEvent.VK_F1:\r
+ try\r
+ {\r
+ ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();\r
+ java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");\r
+ javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);\r
+\r
+ javax.help.HelpBroker hb = hs.createHelpBroker();\r
+ hb.setCurrentID("home");\r
+ hb.setDisplayed(true);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ break;\r
+\r
}\r
}\r
});\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
public void fontChanged()\r
{\r
// set idCanvas bufferedImage to null\r
av.charHeight + fm.getDescent()));\r
\r
idPanel.idCanvas.gg = null;\r
+ seqPanel.seqCanvas.img = null;\r
annotationPanel.adjustPanelHeight();\r
\r
Dimension d = calculateIdWidth();\r
d.setSize(d.width + 4, d.height);\r
idPanel.idCanvas.setPreferredSize(d);\r
hscrollFillerPanel.setPreferredSize(d);\r
+\r
+ if (av.getWrapAlignment())\r
+ {\r
+ int max = av.alignment.getWidth() /\r
+ seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\r
+ vscroll.setMaximum(max);\r
+ vscroll.setUnitIncrement(1);\r
+ vscroll.setVisibleAmount(1);\r
+ }\r
+ else\r
+ {\r
+ setScrollValues(av.getStartRes(), av.getStartSeq());\r
+ }\r
+\r
+ if (overviewPanel != null)\r
+ overviewPanel.setBoxPosition();\r
+\r
repaint();\r
}\r
\r
- Dimension calculateIdWidth()\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Dimension calculateIdWidth()\r
{\r
- Graphics g = this.getGraphics();\r
+ Container c = new Container();\r
\r
- if (g == null)\r
- {\r
- javax.swing.JFrame f = new javax.swing.JFrame();\r
- f.addNotify();\r
- g = f.getGraphics();\r
- }\r
-\r
- FontMetrics fm = g.getFontMetrics(av.font);\r
+ FontMetrics fm = c.getFontMetrics(av.font);\r
AlignmentI al = av.getAlignment();\r
\r
int i = 0;\r
{\r
SequenceI s = al.getSequenceAt(i);\r
\r
- if (av.getShowFullId())\r
- {\r
- id = s.getDisplayId();\r
- }\r
- else\r
- {\r
- id = s.getName();\r
- }\r
+ id = s.getDisplayId(av.getShowJVSuffix());\r
\r
if (fm.stringWidth(id) > idWidth)\r
{\r
\r
if (al.getAlignmentAnnotation() != null)\r
{\r
- fm = g.getFontMetrics(alabels.getFont());\r
+ fm = c.getFontMetrics(alabels.getFont());\r
\r
while (i < al.getAlignmentAnnotation().length)\r
{\r
return new Dimension(idWidth, 12);\r
}\r
\r
- public void highlightSearchResults(int[] results)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param results DOCUMENT ME!\r
+ */\r
+ public void highlightSearchResults(SearchResults results)\r
{\r
seqPanel.seqCanvas.highlightSearchResults(results);\r
\r
// do we need to scroll the panel?\r
if (results != null)\r
{\r
- SequenceI seq = av.alignment.getSequenceAt(results[0]);\r
- int start = seq.findIndex(results[1]) - 1;\r
- int end = seq.findIndex(results[2]) - 1;\r
+ SequenceI seq = results.getResultSequence(0);\r
+ int seqIndex = av.alignment.findIndex(seq);\r
+ int start = seq.findIndex(results.getResultStart(0)) - 1;\r
+ int end = seq.findIndex(results.getResultEnd(0)) - 1;\r
\r
- if ( (av.getStartRes() > start) || (av.getEndRes() < end) ||\r
- ( (av.getStartSeq() > results[0]) ||\r
- (av.getEndSeq() < results[0])))\r
+ if(!av.wrapAlignment)\r
+ {\r
+ if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||\r
+ ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))\r
+ {\r
+ setScrollValues(start, seqIndex);\r
+ }\r
+ }\r
+ else\r
{\r
- setScrollValues(start, results[0]);\r
+ scrollToWrappedVisible(start);\r
}\r
}\r
}\r
\r
+ void scrollToWrappedVisible(int res)\r
+ {\r
+ int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\r
+ if( res<=av.getStartRes() || res>=(av.getStartRes()+cwidth) )\r
+ {\r
+ vscroll.setValue(res / cwidth);\r
+ av.startRes = vscroll.getValue() * cwidth;\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public OverviewPanel getOverviewPanel()\r
{\r
return overviewPanel;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param op DOCUMENT ME!\r
+ */\r
public void setOverviewPanel(OverviewPanel op)\r
{\r
overviewPanel = op;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param b DOCUMENT ME!\r
+ */\r
public void setAnnotationVisible(boolean b)\r
{\r
- annotationSpaceFillerHolder.setVisible(b);\r
- annotationScroller.setVisible(b);\r
+ if (!av.wrapAlignment)\r
+ {\r
+ annotationSpaceFillerHolder.setVisible(b);\r
+ annotationScroller.setVisible(b);\r
+ }\r
+ repaint();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param wrap DOCUMENT ME!\r
+ */\r
public void setWrapAlignment(boolean wrap)\r
{\r
+ av.startSeq = 0;\r
scalePanelHolder.setVisible(!wrap);\r
hscroll.setVisible(!wrap);\r
idwidthAdjuster.setVisible(!wrap);\r
\r
- av.setShowAnnotation(!wrap);\r
- annotationScroller.setVisible(!wrap);\r
- annotationSpaceFillerHolder.setVisible(!wrap);\r
- idSpaceFillerPanel1.setVisible(!wrap);\r
-\r
- repaint();\r
- }\r
-\r
- public void setColourScheme()\r
- {\r
- ColourSchemeI cs = av.getGlobalColourScheme();\r
-\r
- if (av.getConservationSelected())\r
+ if (wrap)\r
{\r
- Alignment al = (Alignment) av.getAlignment();\r
- Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3,\r
- al.getSequences(), 0,\r
- al.getWidth());\r
-\r
- c.calculate();\r
- c.verdict(false, av.ConsPercGaps);\r
-\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, cs);\r
-\r
- av.setGlobalColourScheme(ccs);\r
+ annotationScroller.setVisible(false);\r
+ annotationSpaceFillerHolder.setVisible(false);\r
+ }\r
+ else if (av.showAnnotation)\r
+ {\r
+ annotationScroller.setVisible(true);\r
+ annotationSpaceFillerHolder.setVisible(true);\r
}\r
\r
+ idSpaceFillerPanel1.setVisible(!wrap);\r
+\r
repaint();\r
}\r
\r
return true;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param right DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public boolean scrollRight(boolean right)\r
{\r
- if (right)\r
+ if (!right)\r
{\r
if (hscroll.getValue() < 1)\r
{\r
return true;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param x DOCUMENT ME!\r
+ * @param y DOCUMENT ME!\r
+ */\r
public void setScrollValues(int x, int y)\r
{\r
- av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -\r
- 1);\r
+\r
+ int width = av.alignment.getWidth();\r
+ int height = av.alignment.getHeight();\r
+\r
+ if(av.hasHiddenColumns)\r
+ width = av.getColumnSelection().findColumnPosition(width);\r
+\r
+ av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) -1);\r
\r
hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;\r
vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;\r
\r
- if (hextent > av.alignment.getWidth())\r
+ if (hextent > width)\r
{\r
- hextent = av.alignment.getWidth();\r
+ hextent = width;\r
}\r
\r
- if (vextent > av.alignment.getHeight())\r
+ if (vextent > height)\r
{\r
- vextent = av.alignment.getHeight();\r
+ vextent = height;\r
}\r
\r
- if ( (hextent + x) > av.getAlignment().getWidth())\r
+ if ( (hextent + x) > width)\r
{\r
- x = av.getAlignment().getWidth() - hextent;\r
+ x = width - hextent;\r
}\r
\r
- if ( (vextent + y) > av.getAlignment().getHeight())\r
+ if ( (vextent + y) > height)\r
{\r
- y = av.getAlignment().getHeight() - vextent;\r
+ y = height - vextent;\r
}\r
\r
if (y < 0)\r
x = 0;\r
}\r
\r
- hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());\r
- vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());\r
+ hscroll.setValues(x, hextent, 0, width);\r
+ vscroll.setValues(y, vextent, 0, height);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
public void adjustmentValueChanged(AdjustmentEvent evt)\r
{\r
int oldX = av.getStartRes();\r
overviewPanel.setBoxPosition();\r
}\r
\r
+ int scrollX = av.startRes - oldX;\r
+ int scrollY = av.startSeq - oldY;\r
+\r
if (av.getWrapAlignment() || !fastPaint)\r
{\r
repaint();\r
}\r
else\r
{\r
- idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);\r
- seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,\r
- av.getStartSeq() - oldY);\r
-\r
- scalePanel.repaint();\r
-\r
- if (av.getShowAnnotation())\r
+ // Make sure we're not trying to draw a panel\r
+ // larger than the visible window\r
+ if(scrollX>av.endRes-av.startRes)\r
+ scrollX = av.endRes-av.startRes;\r
+ else if(scrollX<av.startRes-av.endRes)\r
+ scrollX = av.startRes - av.endRes;\r
+\r
+ if(scrollX!=0 || scrollY!=0)\r
{\r
- annotationPanel.fastPaint(av.getStartRes() - oldX);\r
+ idPanel.idCanvas.fastPaint(scrollY);\r
+ seqPanel.seqCanvas.fastPaint(scrollX,\r
+ scrollY);\r
+ scalePanel.repaint();\r
+\r
+ if (av.getShowAnnotation())\r
+ {\r
+ annotationPanel.fastPaint(scrollX);\r
+ }\r
}\r
}\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ */\r
public void paintComponent(Graphics g)\r
{\r
invalidate();\r
if (av.getWrapAlignment())\r
{\r
int max = av.alignment.getWidth() /\r
- seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\r
+ seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) +1;\r
+\r
+\r
vscroll.setMaximum(max);\r
vscroll.setUnitIncrement(1);\r
vscroll.setVisibleAmount(1);\r
{\r
setScrollValues(av.getStartRes(), av.getStartSeq());\r
}\r
+\r
+ if( this.getVisibleRect().getBounds() == g.getClipBounds()\r
+ && overviewPanel != null)\r
+ overviewPanel.updateOverviewImage();\r
+\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param pg DOCUMENT ME!\r
+ * @param pf DOCUMENT ME!\r
+ * @param pi DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ *\r
+ * @throws PrinterException DOCUMENT ME!\r
+ */\r
public int print(Graphics pg, PageFormat pf, int pi)\r
throws PrinterException\r
{\r
}\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param pg DOCUMENT ME!\r
+ * @param pwidth DOCUMENT ME!\r
+ * @param pheight DOCUMENT ME!\r
+ * @param pi DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ *\r
+ * @throws PrinterException DOCUMENT ME!\r
+ */\r
public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)\r
throws PrinterException\r
{\r
\r
if (av.showAnnotation)\r
{\r
- pagesHigh += annotationPanel.getHeight();\r
+ pagesHigh += annotationPanel.adjustPanelHeight() + 3;\r
}\r
\r
pagesHigh /= pheight;\r
Color currentColor = null;\r
Color currentTextColor = null;\r
\r
+ pg.setFont(new Font(av.getFont().getName(),\r
+ Font.ITALIC,\r
+ av.getFont().getSize()));\r
for (int i = startSeq; i < endSeq; i++)\r
{\r
if ( (av.getSelectionGroup() != null) &&\r
}\r
\r
pg.setColor(currentColor);\r
- pg.fillRect(0,\r
- jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,\r
- av.getCharHeight()), idWidth, av.getCharHeight());\r
+ pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,\r
+ av.getCharHeight());\r
\r
pg.setColor(currentTextColor);\r
\r
- String string = av.getAlignment().getSequenceAt(i).getName();\r
-\r
- if (av.getShowFullId())\r
- {\r
- string = av.getAlignment().getSequenceAt(i).getDisplayId();\r
- }\r
+ String string = av.getAlignment().getSequenceAt(i).getDisplayId\r
+ ( av.getShowJVSuffix());\r
\r
pg.drawString(string, 0,\r
- (jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,\r
- av.getCharHeight()) + av.getCharHeight()) -\r
+ ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -\r
(av.getCharHeight() / 5));\r
}\r
\r
+ pg.setFont(av.getFont());\r
+\r
// draw main sequence panel\r
pg.translate(idWidth, 0);\r
- seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,\r
- startRes, startSeq, 0);\r
+ seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);\r
\r
if (av.showAnnotation && (endSeq == av.alignment.getHeight()))\r
{\r
- pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight);\r
- alabels.drawComponent( (Graphics2D) pg);\r
- pg.translate(idWidth, 0);\r
+ pg.translate( -idWidth-3, (endSeq - startSeq) * av.charHeight + 3);\r
+ alabels.drawComponent( (Graphics2D) pg, idWidth);\r
+ pg.translate(idWidth+3, 0);\r
annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +\r
1);\r
}\r
return Printable.PAGE_EXISTS;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param pg DOCUMENT ME!\r
+ * @param pwidth DOCUMENT ME!\r
+ * @param pheight DOCUMENT ME!\r
+ * @param pi DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ *\r
+ * @throws PrinterException DOCUMENT ME!\r
+ */\r
public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,\r
int pi)\r
throws PrinterException\r
{\r
+\r
+ int annotationHeight = 0;\r
+ AnnotationLabels labels = null;\r
+ if (av.showAnnotation)\r
+ {\r
+ annotationHeight = annotationPanel.adjustPanelHeight();\r
+ labels = new AnnotationLabels(av);\r
+ }\r
+\r
+ int hgap = av.charHeight;\r
+ if (av.scaleAboveWrapped)\r
+ hgap += av.charHeight;\r
+\r
+ int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+ + hgap\r
+ + annotationHeight;\r
+\r
int idWidth = calculateIdWidth().width + 4;\r
\r
int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -\r
idWidth);\r
- int totalHeight = totalHeight = (av.alignment.getHeight() + 2) *\r
- ( (av.alignment.getWidth() / resWidth) +\r
- 1) * av.charHeight;\r
+\r
+ int totalHeight = cHeight * (av.alignment.getWidth() / resWidth + 1);\r
\r
pg.setColor(Color.white);\r
pg.fillRect(0, 0, pwidth, pheight);\r
\r
pg.setClip(0, pi * pheight, pwidth, pheight);\r
\r
- int ypos = 2 * av.charHeight;\r
+ int ypos = hgap;\r
+ Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
+ av.getFont().getSize());\r
+ pg.setFont(italic);\r
\r
do\r
{\r
for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
SequenceI s = av.alignment.getSequenceAt(i);\r
- String string = s.getName();\r
-\r
- if (av.getShowFullId())\r
- {\r
- string = s.getDisplayId();\r
- }\r
+ String string = s.getDisplayId( av.getShowJVSuffix());\r
\r
pg.drawString(string, 0,\r
- (AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +\r
- av.charHeight) - (av.charHeight / 5));\r
+ ( (i * av.charHeight) + ypos + av.charHeight) -\r
+ (av.charHeight / 5));\r
+ }\r
+ if (labels != null)\r
+ {\r
+ pg.translate(-3,\r
+ ypos +\r
+ (av.getAlignment().getHeight() * av.charHeight));\r
+\r
+ pg.setFont(av.getFont());\r
+ labels.drawComponent(pg, idWidth);\r
+ pg.setFont(italic);\r
+ pg.translate(+3,\r
+ -ypos -\r
+ (av.getAlignment().getHeight() * av.charHeight));\r
}\r
\r
- ypos += ( (av.alignment.getHeight() + 2) * av.charHeight);\r
+ ypos += cHeight;\r
}\r
while (ypos < totalHeight);\r
\r
if ( (pi * pheight) < totalHeight)\r
{\r
return Printable.PAGE_EXISTS;\r
+\r
}\r
else\r
{\r
}\r
}\r
\r
- public void makeEPS()\r
+ void makeAlignmentImage(int type, File file)\r
{\r
- int height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *\r
- av.chunkHeight;\r
- int width = seqPanel.getWidth() + idPanel.getWidth();\r
+ int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;\r
+ int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);\r
\r
- if (!av.getWrapAlignment())\r
+ if (idPanel.getWidth() == 0)\r
{\r
- height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;\r
- width = idPanel.getWidth() +\r
- (av.alignment.getWidth() * av.charWidth);\r
+ width += calculateIdWidth().getWidth() + 4;\r
}\r
\r
- if (av.getShowAnnotation())\r
+ if (av.getWrapAlignment())\r
{\r
- height += annotationPanel.getPreferredSize().height;\r
+ height = getWrappedHeight();\r
+ width = seqPanel.getWidth() + idPanel.getWidth();\r
}\r
-\r
- try\r
+ else if (av.getShowAnnotation())\r
{\r
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
- jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"), new String[]\r
- {"eps"},\r
- new String[]\r
- {"Encapsulated Postscript"},\r
- "Encapsulated Postscript");\r
- chooser.setFileView(new jalview.io.JalviewFileView());\r
- chooser.setDialogTitle("Create EPS file from alignment");\r
- chooser.setToolTipText("Save");\r
-\r
- int value = chooser.showSaveDialog(this);\r
-\r
- if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- return;\r
- }\r
-\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
- chooser.getSelectedFile().getParent());\r
+ height += annotationPanel.adjustPanelHeight() + 3;\r
+ }\r
\r
- FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
- EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width,\r
- height);\r
+ jalview.util.ImageMaker im;\r
+ if(type==jalview.util.ImageMaker.PNG)\r
+ im = new jalview.util.ImageMaker(this,\r
+ jalview.util.ImageMaker.PNG,\r
+ "Create PNG image from alignment",\r
+ width, height, file, null);\r
+ else\r
+ im = new jalview.util.ImageMaker(this,\r
+ jalview.util.ImageMaker.EPS,\r
+ "Create EPS file from alignment",\r
+ width, height, file, alignFrame.getTitle() );\r
\r
+ try\r
+ {\r
if (av.getWrapAlignment())\r
{\r
- printWrappedAlignment(pg, width, height, 0);\r
+ if(im.getGraphics()!=null)\r
+ {\r
+ printWrappedAlignment(im.getGraphics(), width, height, 0);\r
+ im.writeImage();\r
+ }\r
}\r
else\r
{\r
- printUnwrapped(pg, width, height, 0);\r
+ if(im.getGraphics()!=null)\r
+ {\r
+ printUnwrapped(im.getGraphics(), width, height, 0);\r
+ im.writeImage();\r
+ }\r
}\r
+ }\r
+ catch (OutOfMemoryError err)\r
+ {\r
+ System.out.println("########################\n"\r
+ + "OUT OF MEMORY " + file + "\n"\r
+ + "########################");\r
+\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Out of Memory Creating Image!!"\r
+ +\r
+ "\nSee help files for increasing Java Virtual Machine memory."\r
+ , "Out of memory",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ System.out.println("Create IMAGE: " + err);\r
+ System.gc();\r
\r
- pg.flush();\r
- pg.close();\r
}\r
catch (Exception ex)\r
{\r
ex.printStackTrace();\r
}\r
}\r
-\r
- public void makePNG()\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void makeEPS(File epsFile)\r
{\r
- int height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *\r
- av.chunkHeight;\r
- int width = seqPanel.getWidth() + idPanel.getWidth();\r
+ makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);\r
+ }\r
\r
- if (!av.getWrapAlignment())\r
- {\r
- height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;\r
- width = idPanel.getWidth() +\r
- (av.alignment.getWidth() * av.charWidth);\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void makePNG(File pngFile)\r
+ {\r
+ makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);\r
+ }\r
\r
- if (av.getShowAnnotation())\r
- {\r
- height += annotationPanel.getPreferredSize().height;\r
- }\r
+ public void makePNGImageMap(File imgMapFile, String imageName)\r
+ {\r
+ ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS\r
+ //////////////////////////////////////////////\r
+ int idWidth = calculateIdWidth().width + 4;\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+ int scaleHeight = av.charHeight + fm.getDescent();\r
\r
- try\r
+ // Gen image map\r
+ //////////////////////////////////\r
+ if (imgMapFile != null)\r
{\r
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
- jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"), new String[]\r
- {"png"},\r
- new String[]\r
- {"Portable network graphics"},\r
- "Portable network graphics");\r
- chooser.setFileView(new jalview.io.JalviewFileView());\r
- chooser.setDialogTitle("Create EPS file from alignment");\r
- chooser.setToolTipText("Save");\r
-\r
- int value = chooser.showSaveDialog(this);\r
+ try\r
+ {\r
+ int s, sSize = av.alignment.getHeight(),\r
+ res, alwidth = av.alignment.getWidth(), g, gSize, f, fSize, sy;\r
+ StringBuffer text = new StringBuffer();\r
+ PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));\r
+ out.println(jalview.io.HTMLOutput.getImageMapHTML());\r
+ out.println("<img src=\"" + imageName +\r
+ "\" border=\"0\" usemap=\"#Map\" >"\r
+ + "<map name=\"Map\">");\r
+\r
+ for (s = 0; s < sSize; s++)\r
+ {\r
+ sy = s * av.charHeight + scaleHeight;\r
+\r
+ SequenceI seq = av.alignment.getSequenceAt(s);\r
+ SequenceFeature [] features = seq.getDatasetSequence().getSequenceFeatures();\r
+ SequenceGroup[] groups = av.alignment.findAllGroups(seq);\r
+ for(res =0; res<alwidth; res++)\r
+ {\r
+ text = new StringBuffer();\r
+ Object obj = null;\r
+ if(av.alignment.isNucleotide())\r
+ obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)+"" );\r
+ else\r
+ obj = ResidueProperties.aa2Triplet.get(\r
+ seq.getCharAt(res) + "");\r
+\r
+ if (obj == null)\r
+ continue;\r
+\r
+ String triplet = obj.toString();\r
+ int alIndex = seq.findPosition(res);\r
+ gSize = groups.length;\r
+ for (g = 0; g < gSize; g++)\r
+ {\r
+ if(text.length()<1)\r
+ {\r
+ text.append("<area shape=\"rect\" coords=\""\r
+ + (idWidth + res * av.charWidth) + ","\r
+ + sy + ","\r
+ + (idWidth + (res + 1) * av.charWidth) + ","\r
+ + (av.charHeight + sy) + "\""\r
+ + " onMouseOver=\"toolTip('"\r
+ + alIndex + " " + triplet );\r
+ }\r
+\r
+ if(groups[g].getStartRes()<res && groups[g].getEndRes()>res)\r
+ text.append("<br><em>" + groups[g].getName() + "</em>");\r
+ }\r
+\r
+ if (features != null)\r
+ {\r
+ if(text.length()<1)\r
+ {\r
+ text.append("<area shape=\"rect\" coords=\""\r
+ + (idWidth + res * av.charWidth) + ","\r
+ + sy + ","\r
+ + (idWidth + (res + 1) * av.charWidth) + ","\r
+ + (av.charHeight + sy) + "\""\r
+ + " onMouseOver=\"toolTip('"\r
+ + alIndex + " " + triplet );\r
+ }\r
+ fSize = features.length;\r
+ for (f = 0; f < fSize; f++)\r
+ {\r
+\r
+ if ( (features[f].getBegin() <= seq.findPosition(res)) &&\r
+ (features[f].getEnd() >= seq.findPosition(res)))\r
+ {\r
+ if (features[f].getType().equals("disulfide bond"))\r
+ {\r
+ if (features[f].getBegin() == seq.findPosition(res)\r
+ || features[f].getEnd() == seq.findPosition(res))\r
+ {\r
+ text.append("<br>disulfide bond " + features[f].getBegin() + ":" +\r
+ features[f].getEnd());\r
+ }\r
+ }\r
+ else\r
+ {\r
+ text.append("<br>");\r
+ text.append(features[f].getType());\r
+ if (features[f].getDescription() != null && !features[f].getType().equals(features[f].getDescription()))\r
+ text.append(" " + features[f].getDescription());\r
+\r
+ if (features[f].getStatus() != null && features[f].getStatus().length()>0)\r
+ {\r
+ text.append(" (" + features[f].getStatus() + ")");\r
+ }\r
+ }\r
+ }\r
+\r
+ }\r
+ }\r
+ if(text.length()>1)\r
+ {\r
+ text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");\r
+ out.println(text.toString());\r
+ }\r
+ }\r
+ }\r
+ out.println("</map></body></html>");\r
+ out.close();\r
\r
- if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
+ }\r
+ catch (Exception ex)\r
{\r
- return;\r
+ ex.printStackTrace();\r
}\r
+ } ///////////END OF IMAGE MAP\r
\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
- chooser.getSelectedFile().getParent());\r
-\r
- FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
+ }\r
\r
- BufferedImage bi = new BufferedImage(width, height,\r
- BufferedImage.TYPE_INT_RGB);\r
- Graphics2D png = (Graphics2D) bi.getGraphics();\r
+ int getWrappedHeight()\r
+ {\r
\r
- png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
- RenderingHints.VALUE_ANTIALIAS_ON);\r
+ int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(\r
+ seqPanel.seqCanvas.getWidth());\r
\r
- if (av.getWrapAlignment())\r
- {\r
- printWrappedAlignment(png, width, height, 0);\r
- }\r
- else\r
- {\r
- printUnwrapped(png, width, height, 0);\r
- }\r
+ int hgap = av.charHeight;\r
+ if (av.scaleAboveWrapped)\r
+ hgap += av.charHeight;\r
\r
- ImageIO.write(bi, "png", out);\r
- out.close();\r
- }\r
- catch (Exception ex)\r
+ int annotationHeight = 0;\r
+ if (av.showAnnotation)\r
{\r
- ex.printStackTrace();\r
+ annotationHeight = annotationPanel.adjustPanelHeight();\r
}\r
- }\r
-}\r
\r
-class Preview\r
- extends JFrame\r
-{\r
- public Preview(Image image)\r
- {\r
- setResizable(true);\r
- setSize(image.getWidth(this), image.getHeight(this));\r
- setVisible(true);\r
- getContentPane().setLayout(new BorderLayout());\r
- getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);\r
- validate();\r
- repaint();\r
- }\r
-}\r
+ int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+ + hgap\r
+ + annotationHeight;\r
\r
-class PreviewPanel\r
- extends JPanel\r
-{\r
- Image image;\r
+ int height = ( (av.alignment.getWidth() / chunkWidth) + 1) * cHeight;\r
\r
- public PreviewPanel(Image image)\r
+ return height;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+ class Preview\r
+ extends JFrame\r
{\r
- this.image = image;\r
+ /**\r
+ * Creates a new Preview object.\r
+ *\r
+ * @param image DOCUMENT ME!\r
+ */\r
+ public Preview(Image image)\r
+ {\r
+ setResizable(true);\r
+ setSize(image.getWidth(this), image.getHeight(this));\r
+ setVisible(true);\r
+ getContentPane().setLayout(new BorderLayout());\r
+ getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);\r
+ validate();\r
+ repaint();\r
+ }\r
}\r
\r
- public void paintComponent(Graphics g)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+ class PreviewPanel\r
+ extends JPanel\r
{\r
- if (image != null)\r
+ Image image;\r
+\r
+ /**\r
+ * Creates a new PreviewPanel object.\r
+ *\r
+ * @param image DOCUMENT ME!\r
+ */\r
+ public PreviewPanel(Image image)\r
{\r
- g.drawImage(image, 0, 0, this);\r
+ this.image = image;\r
}\r
- else\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ */\r
+ public void paintComponent(Graphics g)\r
{\r
- System.out.println("DEBUG:image is null");\r
+ if (image != null)\r
+ {\r
+ g.drawImage(image, 0, 0, this);\r
+ }\r
+ else\r
+ {\r
+ System.out.println("DEBUG:image is null");\r
+ }\r
}\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff