/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
*/\r
package jalview.gui;\r
\r
-import jalview.datamodel.*;\r
-\r
-import jalview.jbgui.*;\r
-\r
-import jalview.schemes.*;\r
+import java.beans.*;\r
+import java.io.*;\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
import java.awt.print.*;\r
-\r
-import java.io.*;\r
-\r
import javax.swing.*;\r
\r
+import jalview.datamodel.*;\r
+import jalview.jbgui.*;\r
+import jalview.schemes.*;\r
\r
/**\r
* DOCUMENT ME!\r
* @author $author$\r
* @version $Revision$\r
*/\r
-public class AlignmentPanel extends GAlignmentPanel\r
- implements AdjustmentListener, Printable\r
+public class AlignmentPanel\r
+ extends GAlignmentPanel implements AdjustmentListener, Printable\r
{\r
public AlignViewport av;\r
OverviewPanel overviewPanel;\r
annotationPanel = new AnnotationPanel(this);\r
alabels = new AnnotationLabels(this);\r
\r
-\r
annotationScroller.setViewportView(annotationPanel);\r
annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);\r
\r
- fontChanged();\r
-\r
scalePanelHolder.add(scalePanel, BorderLayout.CENTER);\r
seqPanelHolder.add(seqPanel, BorderLayout.CENTER);\r
\r
setScrollValues(0, 0);\r
\r
- adjustAnnotationHeight();\r
-\r
setAnnotationVisible(av.getShowAnnotation());\r
\r
hscroll.addAdjustmentListener(this);\r
vscroll.addAdjustmentListener(this);\r
\r
- af.addKeyListener(new KeyAdapter()\r
+ final AlignmentPanel ap = this;\r
+ av.addPropertyChangeListener(new PropertyChangeListener()\r
{\r
- public void keyPressed(KeyEvent evt)\r
+ public void propertyChange(PropertyChangeEvent evt)\r
{\r
- if(av.cursorMode\r
- && evt.getKeyCode()>=KeyEvent.VK_0\r
- && evt.getKeyCode()<=KeyEvent.VK_9)\r
+ if (evt.getPropertyName().equals("alignment"))\r
{\r
- seqPanel.numberPressed(evt.getKeyChar());\r
+ PaintRefresher.Refresh(ap,\r
+ av.getSequenceSetId(),\r
+ true,\r
+ true);\r
+ alignmentChanged();\r
}\r
+ }\r
+ });\r
\r
- switch (evt.getKeyCode())\r
- {\r
- case 27: // escape key\r
- alignFrame.deselectAllSequenceMenuItem_actionPerformed(null);\r
-\r
- break;\r
-\r
- case KeyEvent.VK_DOWN:\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
- 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
+ fontChanged();\r
+ adjustAnnotationHeight();\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 && !evt.isControlDown())\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
\r
- case KeyEvent.VK_ENTER:\r
- case KeyEvent.VK_COMMA:\r
- if(av.cursorMode)\r
- {\r
- seqPanel.setCursorRowAndColumn();\r
- }\r
- break;\r
+ public void alignmentChanged()\r
+ {\r
+ av.alignmentChanged(this);\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
+ alignFrame.updateEditMenuBar();\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
+ paintAlignment(true);\r
\r
- }\r
- }\r
- });\r
}\r
\r
/**\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
+ {\r
overviewPanel.setBoxPosition();\r
+ }\r
\r
repaint();\r
}\r
{\r
Container c = new Container();\r
\r
- FontMetrics fm = c.getFontMetrics(av.font);\r
+ FontMetrics fm = c.getFontMetrics(\r
+ new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));\r
+\r
AlignmentI al = av.getAlignment();\r
\r
int i = 0;\r
int start = seq.findIndex(results.getResultStart(0)) - 1;\r
int end = seq.findIndex(results.getResultEnd(0)) - 1;\r
\r
- if(!av.wrapAlignment)\r
+ if (!av.wrapAlignment)\r
{\r
- if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||\r
- ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))\r
+ if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||\r
+ ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))\r
{\r
setScrollValues(start, seqIndex);\r
}\r
scrollToWrappedVisible(start);\r
}\r
}\r
+\r
+ paintAlignment(true);\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
+ int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.\r
+ getWidth());\r
+ if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))\r
{\r
vscroll.setValue(res / cwidth);\r
av.startRes = vscroll.getValue() * cwidth;\r
\r
public void adjustAnnotationHeight()\r
{\r
- javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ if (alignFrame.getHeight() == 0)\r
{\r
- public void run()\r
- {\r
- while(alignFrame.getHeight()==0)\r
- {\r
- Thread.yield();\r
- }\r
+ System.out.println("NEEDS FIXING");\r
+ }\r
\r
- int height = annotationPanel.adjustPanelHeight();\r
+ int height = annotationPanel.adjustPanelHeight();\r
\r
- if (height > alignFrame.getHeight() / 2)\r
- {\r
- height = alignFrame.getHeight() / 2;\r
- }\r
+ if (hscroll.isVisible())\r
+ {\r
+ height += hscroll.getPreferredSize().height;\r
+ }\r
+ if (height > alignFrame.getHeight() / 2)\r
+ {\r
+ height = alignFrame.getHeight() / 2;\r
+ }\r
\r
- annotationScroller.setPreferredSize(\r
- new Dimension(annotationScroller.getWidth(),\r
- height));\r
+ hscroll.addNotify();\r
\r
- annotationSpaceFillerHolder.setPreferredSize(new Dimension(\r
- annotationSpaceFillerHolder.getWidth(),\r
- height));\r
+ annotationScroller.setPreferredSize(\r
+ new Dimension(annotationScroller.getWidth(), height));\r
\r
- annotationPanel.repaint();\r
- }\r
- });\r
+\r
+ annotationSpaceFillerHolder.setPreferredSize(new Dimension(\r
+ annotationSpaceFillerHolder.getWidth(),\r
+ height));\r
+\r
+ repaint();\r
}\r
\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
+ if (av.hasHiddenColumns)\r
+ {\r
+ width = av.getColumnSelection().findColumnPosition(width);\r
+ }\r
\r
- av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) -1);\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 (av.getWrapAlignment())\r
{\r
- if(offy>-1)\r
+ if (offy > -1)\r
{\r
int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.\r
seqCanvas.getWidth());\r
//was wrapped when saved and user has wrap alignment true\r
//as preference setting\r
SwingUtilities.invokeLater(new Runnable()\r
- {\r
- public void run()\r
- {\r
- setScrollValues(av.getStartRes(), av.getStartSeq());\r
- }\r
- });\r
+ {\r
+ public void run()\r
+ {\r
+ setScrollValues(av.getStartRes(), av.getStartSeq());\r
+ }\r
+ });\r
}\r
}\r
else\r
{\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
+ if (scrollX > av.endRes - av.startRes)\r
+ {\r
+ scrollX = av.endRes - av.startRes;\r
+ }\r
+ else if (scrollX < av.startRes - av.endRes)\r
+ {\r
scrollX = av.startRes - av.endRes;\r
+ }\r
\r
- if(scrollX!=0 || scrollY!=0)\r
+ if (scrollX != 0 || scrollY != 0)\r
{\r
idPanel.idCanvas.fastPaint(scrollY);\r
seqPanel.seqCanvas.fastPaint(scrollX,\r
}\r
}\r
\r
+ public void paintAlignment(boolean updateOverview)\r
+ {\r
+ repaint();\r
+\r
+ if(updateOverview)\r
+ {\r
+ jalview.structure.StructureSelectionManager.getStructureSelectionManager()\r
+ .sequenceColoursChanged(this);\r
+\r
+ if (overviewPanel != null)\r
+ {\r
+ overviewPanel.updateOverviewImage();\r
+ }\r
+ }\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
int maxwidth = av.alignment.getWidth();\r
\r
if (av.hasHiddenColumns)\r
+ {\r
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+ }\r
\r
- int max = maxwidth /\r
- seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) +\r
- 1;\r
-\r
-\r
- vscroll.setMaximum(max);\r
- vscroll.setUnitIncrement(1);\r
- vscroll.setVisibleAmount(1);\r
+ int canvasWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.\r
+ seqCanvas.getWidth());\r
+ if (canvasWidth > 0)\r
+ {\r
+ int max = maxwidth /\r
+ seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.\r
+ getWidth()) +\r
+ 1;\r
+ vscroll.setMaximum(max);\r
+ vscroll.setUnitIncrement(1);\r
+ vscroll.setVisibleAmount(1);\r
+ }\r
}\r
else\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
public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)\r
throws PrinterException\r
{\r
- int idWidth = calculateIdWidth().width + 4;\r
+ int idWidth = getVisibleIdWidth();\r
FontMetrics fm = getFontMetrics(av.getFont());\r
int scaleHeight = av.charHeight + fm.getDescent();\r
\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
+ pg.setFont(idPanel.idCanvas.idfont);\r
+\r
+ SequenceI seq;\r
for (int i = startSeq; i < endSeq; i++)\r
{\r
+ seq = av.getAlignment().getSequenceAt(i);\r
if ( (av.getSelectionGroup() != null) &&\r
- av.getSelectionGroup().getSequences(false).contains(\r
- av.getAlignment().getSequenceAt(i)))\r
+ av.getSelectionGroup().getSequences(null).contains(seq))\r
{\r
currentColor = Color.gray;\r
currentTextColor = Color.black;\r
}\r
else\r
{\r
- currentColor = av.getAlignment().getSequenceAt(i).getColor();\r
+ currentColor = av.getSequenceColour(seq);\r
currentTextColor = Color.black;\r
}\r
\r
\r
pg.setColor(currentTextColor);\r
\r
- String string = av.getAlignment().getSequenceAt(i).getDisplayId\r
- ( av.getShowJVSuffix());\r
+ int xPos = 0;\r
+ if (av.rightAlignIds)\r
+ {\r
+ fm = pg.getFontMetrics();\r
+ xPos = idWidth - fm.stringWidth(\r
+ seq.getDisplayId(av.getShowJVSuffix())\r
+ ) - 4;\r
+ }\r
\r
- pg.drawString(string, 0,\r
+ pg.drawString(seq.getDisplayId(av.getShowJVSuffix()),\r
+ xPos,\r
( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -\r
(av.getCharHeight() / 5));\r
}\r
\r
if (av.showAnnotation && (endSeq == av.alignment.getHeight()))\r
{\r
- pg.translate( -idWidth-3, (endSeq - startSeq) * av.charHeight + 3);\r
+ pg.translate( -idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);\r
alabels.drawComponent( (Graphics2D) pg, idWidth);\r
- pg.translate(idWidth+3, 0);\r
+ pg.translate(idWidth + 3, 0);\r
annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +\r
1);\r
}\r
\r
int hgap = av.charHeight;\r
if (av.scaleAboveWrapped)\r
+ {\r
hgap += av.charHeight;\r
+ }\r
\r
int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+ hgap\r
+ annotationHeight;\r
\r
- int idWidth = calculateIdWidth().width + 4;\r
+ int idWidth = getVisibleIdWidth();\r
\r
int maxwidth = av.alignment.getWidth();\r
if (av.hasHiddenColumns)\r
+ {\r
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
-\r
+ }\r
\r
int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -\r
idWidth);\r
pg.setClip(0, pi * pheight, pwidth, pheight);\r
\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
+ pg.setFont(idPanel.idCanvas.idfont);\r
SequenceI s = av.alignment.getSequenceAt(i);\r
- String string = s.getDisplayId( av.getShowJVSuffix());\r
-\r
- pg.drawString(string, 0,\r
+ String string = s.getDisplayId(av.getShowJVSuffix());\r
+ int xPos = 0;\r
+ if (av.rightAlignIds)\r
+ {\r
+ FontMetrics fm = pg.getFontMetrics();\r
+ xPos = idWidth - fm.stringWidth(string) - 4;\r
+ }\r
+ pg.drawString(string, xPos,\r
( (i * av.charHeight) + ypos + av.charHeight) -\r
(av.charHeight / 5));\r
}\r
if (labels != null)\r
{\r
- pg.translate(-3,\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
+ pg.translate( +3,\r
-ypos -\r
(av.getAlignment().getHeight() * av.charHeight));\r
}\r
}\r
}\r
\r
+ int getVisibleIdWidth()\r
+ {\r
+ return\r
+ idPanel.getWidth() > 0 ? idPanel.getWidth() :\r
+ calculateIdWidth().width + 4;\r
+ }\r
+\r
void makeAlignmentImage(int type, File file)\r
{\r
int maxwidth = av.alignment.getWidth();\r
if (av.hasHiddenColumns)\r
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);\r
-\r
- int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;\r
- int width = idPanel.getWidth() + (maxwidth * av.charWidth);\r
- if (idPanel.getWidth() == 0)\r
{\r
- width += calculateIdWidth().getWidth() + 4;\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);\r
}\r
\r
+ int height = ( (av.alignment.getHeight() + 1) * av.charHeight)\r
+ + scalePanel.getHeight();\r
+ int width = getVisibleIdWidth() + (maxwidth * av.charWidth);\r
+\r
if (av.getWrapAlignment())\r
{\r
height = getWrappedHeight();\r
if (System.getProperty("java.awt.headless") != null\r
&& System.getProperty("java.awt.headless").equals("true"))\r
{\r
- width = alignFrame.getWidth() - 22;\r
+ width = alignFrame.getWidth()\r
+ - vscroll.getPreferredSize().width\r
+ - alignFrame.getInsets().left\r
+ - alignFrame.getInsets().right;\r
}\r
else\r
- width = seqPanel.getWidth() + idPanel.getWidth();\r
+ {\r
+ width = seqPanel.getWidth() + getVisibleIdWidth();\r
+ }\r
\r
}\r
else if (av.getShowAnnotation())\r
height += annotationPanel.adjustPanelHeight() + 3;\r
}\r
\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
+\r
+ jalview.util.ImageMaker im;\r
+ if (type == jalview.util.ImageMaker.PNG)\r
+ {\r
+ im = new jalview.util.ImageMaker(this,\r
+ jalview.util.ImageMaker.PNG,\r
+ "Create PNG image from alignment",\r
+ width, height, file, null);\r
+ }\r
+ else\r
+ {\r
+ im = new jalview.util.ImageMaker(this,\r
+ jalview.util.ImageMaker.EPS,\r
+ "Create EPS file from alignment",\r
+ width, height, file,\r
+ alignFrame.getTitle());\r
+ }\r
+\r
if (av.getWrapAlignment())\r
{\r
- if(im.getGraphics()!=null)\r
+ if (im.getGraphics() != null)\r
{\r
printWrappedAlignment(im.getGraphics(), width, height, 0);\r
im.writeImage();\r
}\r
else\r
{\r
- if(im.getGraphics()!=null)\r
+ if (im.getGraphics() != null)\r
{\r
printUnwrapped(im.getGraphics(), width, height, 0);\r
im.writeImage();\r
ex.printStackTrace();\r
}\r
}\r
+\r
/**\r
* DOCUMENT ME!\r
*/\r
{\r
///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS\r
//////////////////////////////////////////////\r
- int idWidth = calculateIdWidth().width + 4;\r
+ int idWidth = getVisibleIdWidth();\r
FontMetrics fm = getFontMetrics(av.getFont());\r
int scaleHeight = av.charHeight + fm.getDescent();\r
\r
sy = s * av.charHeight + scaleHeight;\r
\r
SequenceI seq = av.alignment.getSequenceAt(s);\r
- SequenceFeature [] features = seq.getDatasetSequence().getSequenceFeatures();\r
+ SequenceFeature[] features = seq.getDatasetSequence().\r
+ getSequenceFeatures();\r
SequenceGroup[] groups = av.alignment.findAllGroups(seq);\r
- for(res =0; res<alwidth; res++)\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
+ if (av.alignment.isNucleotide())\r
+ {\r
+ obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res) +\r
+ "");\r
+ }\r
else\r
+ {\r
obj = ResidueProperties.aa2Triplet.get(\r
- seq.getCharAt(res) + "");\r
+ seq.getCharAt(res) + "");\r
+ }\r
\r
- if (obj == null)\r
- continue;\r
+ if (obj == null)\r
+ {\r
+ continue;\r
+ }\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
+ 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
+ + (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
+ if (groups[g].getStartRes() < res && groups[g].getEndRes() > res)\r
+ {\r
text.append("<br><em>" + groups[g].getName() + "</em>");\r
+ }\r
}\r
\r
if (features != null)\r
{\r
- if(text.length()<1)\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
+ + (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
+ 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
+ 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].getType().equals("disulfide bond"))\r
+ if (features[f].getBegin() == seq.findPosition(res)\r
+ || features[f].getEnd() == seq.findPosition(res))\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
+ text.append("<br>disulfide bond " + features[f].getBegin() +\r
+ ":" +\r
+ features[f].getEnd());\r
}\r
- else\r
+ }\r
+ else\r
+ {\r
+ text.append("<br>");\r
+ text.append(features[f].getType());\r
+ if (features[f].getDescription() != null &&\r
+ !features[f].\r
+ getType().equals(features[f].getDescription()))\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].getValue("status") != null )\r
- {\r
- text.append(" (" + features[f].getValue("status") + ")");\r
- }\r
+ text.append(" " + features[f].getDescription());\r
}\r
- }\r
\r
+ if (features[f].getValue("status") != null)\r
+ {\r
+ text.append(" (" + features[f].getValue("status") + ")");\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
+ 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
{\r
int seqPanelWidth = seqPanel.seqCanvas.getWidth();\r
\r
- //If headless, seqPanel will have 0 width\r
if (System.getProperty("java.awt.headless") != null\r
- && System.getProperty("java.awt.headless").equals("true"))\r
+ && System.getProperty("java.awt.headless").equals("true"))\r
{\r
- int idWidth = calculateIdWidth().width + 4;\r
- seqPanelWidth = alignFrame.getWidth() - idWidth;\r
+ seqPanelWidth = alignFrame.getWidth()\r
+ - getVisibleIdWidth()\r
+ - vscroll.getPreferredSize().width\r
+ - alignFrame.getInsets().left\r
+ - alignFrame.getInsets().right;\r
}\r
\r
int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(\r
seqPanelWidth\r
- );\r
+ );\r
\r
int hgap = av.charHeight;\r
if (av.scaleAboveWrapped)\r
+ {\r
hgap += av.charHeight;\r
+ }\r
\r
int annotationHeight = 0;\r
if (av.showAnnotation)\r
\r
int maxwidth = av.alignment.getWidth();\r
if (av.hasHiddenColumns)\r
+ {\r
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
-\r
+ }\r
\r
int height = ( (maxwidth / chunkWidth) + 1) * cHeight;\r
\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
- /**\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
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
- class PreviewPanel\r
- extends JPanel\r
- {\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
- this.image = image;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param g DOCUMENT ME!\r
- */\r
- public void paintComponent(Graphics g)\r
- {\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