/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 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
-import java.io.*;\r
import javax.swing.*;\r
-import java.beans.*;\r
-\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
fontChanged();\r
\r
scalePanelHolder.add(scalePanel, BorderLayout.CENTER);\r
- seqPanelHolder.add(seqPanel, BorderLayout.CENTER);\r
+ seqPanelHolder.add(seqPanel, BorderLayout.CENTER);\r
\r
setScrollValues(0, 0);\r
\r
alignmentChanged();\r
}\r
}\r
- });\r
+ });\r
\r
adjustAnnotationHeight();\r
\r
av.alignmentChanged(this);\r
\r
if (overviewPanel != null)\r
+ {\r
overviewPanel.updateOverviewImage();\r
+ }\r
\r
alignFrame.updateEditMenuBar();\r
\r
repaint();\r
}\r
\r
-\r
-\r
/**\r
* DOCUMENT ME!\r
*/\r
hscrollFillerPanel.setPreferredSize(d);\r
\r
if (overviewPanel != null)\r
+ {\r
overviewPanel.setBoxPosition();\r
+ }\r
\r
repaint();\r
}\r
Container c = new Container();\r
\r
FontMetrics fm = c.getFontMetrics(\r
- new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));\r
+ new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));\r
\r
AlignmentI al = av.getAlignment();\r
\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
\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
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
int maxwidth = av.alignment.getWidth();\r
\r
if (av.hasHiddenColumns)\r
+ {\r
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+ }\r
\r
- int canvasWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\r
- if(canvasWidth>0)\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
setScrollValues(av.getStartRes(), av.getStartSeq());\r
}\r
\r
- if( this.getVisibleRect().getBounds() == g.getClipBounds()\r
+ if (this.getVisibleRect().getBounds() == g.getClipBounds()\r
&& overviewPanel != null)\r
- overviewPanel.updateOverviewImage();\r
+ {\r
+ overviewPanel.updateOverviewImage();\r
+ }\r
}\r
\r
/**\r
) - 4;\r
}\r
\r
- pg.drawString(seq.getDisplayId( av.getShowJVSuffix()),\r
+ pg.drawString(seq.getDisplayId(av.getShowJVSuffix()),\r
xPos,\r
( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -\r
(av.getCharHeight() / 5));\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
\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
\r
int ypos = hgap;\r
\r
-\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
+ 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
+ xPos = idWidth - fm.stringWidth(string) - 4;\r
}\r
pg.drawString(string, xPos,\r
( (i * av.charHeight) + ypos + av.charHeight) -\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.translate(+3,\r
+ pg.translate( +3,\r
-ypos -\r
(av.getAlignment().getHeight() * av.charHeight));\r
}\r
{\r
int maxwidth = av.alignment.getWidth();\r
if (av.hasHiddenColumns)\r
+ {\r
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);\r
+ }\r
\r
int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;\r
int width = getVisibleIdWidth() + (maxwidth * av.charWidth);\r
- alignFrame.getInsets().right;\r
}\r
else\r
+ {\r
width = seqPanel.getWidth() + getVisibleIdWidth();\r
+ }\r
\r
}\r
else if (av.getShowAnnotation())\r
try\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
+ 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
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].getBegin() == seq.findPosition(res)\r
+ || features[f].getEnd() == seq.findPosition(res))\r
+ {\r
+ text.append("<br>disulfide bond " + features[f].getBegin() +\r
+ ":" +\r
+ features[f].getEnd());\r
+ }\r
+ }\r
+ else\r
{\r
- if (features[f].getType().equals("disulfide bond"))\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
- 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(" " + features[f].getDescription());\r
}\r
- else\r
+\r
+ if (features[f].getValue("status") != null)\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].getValue("status") + ")");\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
+ 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 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
git://source.jalview.org / jalview.git / blobdiff