/*\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) 2006 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
setLayout(null);\r
\r
sr = new SequenceRenderer(av);\r
- sr.renderGaps( false );\r
+ sr.renderGaps = false;\r
+ sr.forOverview = true;\r
fr = new FeatureRenderer(av);\r
\r
-\r
// scale the initial size of overviewpanel to shape of alignment\r
float initialScale = (float) av.alignment.getWidth() / (float) av.alignment.getHeight();\r
\r
{\r
public void mouseDragged(MouseEvent evt)\r
{\r
- if(!av.wrapAlignment)\r
- doMouseDragged(evt);\r
+ if (!av.wrapAlignment)\r
+ {\r
+ boxX = evt.getX();\r
+ boxY = evt.getY();\r
+ checkValid();\r
+ }\r
}\r
});\r
\r
public void mousePressed(MouseEvent evt)\r
{\r
if(!av.wrapAlignment)\r
- doMousePressed(evt);\r
- }\r
-\r
- public void mouseReleased(MouseEvent evt)\r
- {\r
- if(!av.wrapAlignment)\r
- doMouseReleased(evt);\r
+ {\r
+ boxX = evt.getX();\r
+ boxY = evt.getY();\r
+ checkValid();\r
+ }\r
}\r
});\r
\r
updateOverviewImage();\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void doMousePressed(MouseEvent evt)\r
- {\r
- boxX = evt.getX();\r
- boxY = evt.getY();\r
-\r
- checkValid();\r
- repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void doMouseReleased(MouseEvent evt)\r
- {\r
- boxX = evt.getX();\r
- boxY = evt.getY();\r
- checkValid();\r
-\r
- ap.setScrollValues((int) (boxX / scalew / av.getCharWidth()),\r
- (int) (boxY / scaleh / av.getCharHeight()));\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void doMouseDragged(MouseEvent evt)\r
- {\r
- boxX = evt.getX();\r
- boxY = evt.getY();\r
- checkValid();\r
-\r
- ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),\r
- (int) (boxY / scaleh / av.getCharHeight()));\r
- repaint();\r
- }\r
\r
/**\r
* DOCUMENT ME!\r
\r
if (boxX > (width - boxWidth))\r
{\r
- boxX = width - boxWidth;\r
+ if(av.hasHiddenColumns)\r
+ {\r
+ //Try smallest possible box\r
+ boxWidth = (int) ( (av.endRes - av.startRes + 1) *\r
+ av.getCharWidth() * scalew);\r
+ }\r
+ boxX = width - boxWidth;\r
}\r
+\r
+ int col = (int) (boxX / scalew / av.getCharWidth());\r
+ int row = (int) (boxY / scaleh / av.getCharHeight());\r
+\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ if (!av.getColumnSelection().isVisible(col))\r
+ {\r
+ return;\r
+ }\r
+\r
+ col = av.getColumnSelection().findColumnPosition(col);\r
+ }\r
+\r
+ if( av.hasHiddenRows )\r
+ {\r
+ row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(row);\r
+ }\r
+\r
+ ap.setScrollValues( col, row );\r
+\r
}\r
\r
/**\r
}\r
\r
setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));\r
- setBoxPosition();\r
\r
Thread thread = new Thread(this);\r
thread.start();\r
\r
if (av.showSequenceFeatures)\r
{\r
- fr.featuresDisplayed = ap.seqPanel.seqCanvas.getFeatureRenderer().\r
- featuresDisplayed;\r
- //fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;\r
- fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;\r
- fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;\r
+ fr.transferSettings( ap.seqPanel.seqCanvas.getFeatureRenderer() );\r
}\r
\r
int alwidth = av.alignment.getWidth();\r
- int alheight = av.alignment.getHeight();\r
+ int alheight = av.alignment.getHeight()\r
+ +av.alignment.getHiddenSequences().getSize();\r
\r
setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));\r
\r
float sampleRow = (float) alheight / (float) sequencesHeight;\r
\r
int lastcol=-1, lastrow=-1;\r
- Color color = Color.white;\r
- for (int col = 0; col < width; col++)\r
+ int color = Color.white.getRGB();\r
+ int row, col;\r
+ jalview.datamodel.SequenceI seq;\r
+ boolean hiddenRow = false;\r
+ for (row = 0; row < sequencesHeight; row++)\r
{\r
- for (int row = 0; row < sequencesHeight; row++)\r
+ if((int)(row*sampleRow)==lastrow)\r
{\r
+ //No need to recalculate the colours,\r
+ //Just copy from the row above\r
+ for (col = 0; col < width; col++)\r
+ {\r
+ miniMe.setRGB(col, row, miniMe.getRGB(col, row-1));\r
+ }\r
+ continue;\r
+ }\r
+\r
+ lastrow = (int)(row*sampleRow);\r
+\r
+ hiddenRow = false;\r
+ if (av.hasHiddenRows)\r
+ {\r
+ seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);\r
+ if (seq == null)\r
+ {\r
+ int index =\r
+ av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(lastrow);\r
+\r
+ seq = av.alignment.getSequenceAt(index);\r
+ }\r
+ else\r
+ {\r
+ hiddenRow = true;\r
+ }\r
+ }\r
+ else\r
+ seq = av.alignment.getSequenceAt(lastrow);\r
+\r
+ if(seq==null)\r
+ {\r
+ System.out.println(lastrow+" null");\r
+ continue;\r
+ }\r
+\r
+ for (col = 0; col < width; col++)\r
+ {\r
if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)\r
{\r
- miniMe.setRGB(col,row,color.getRGB());\r
+ miniMe.setRGB(col,row,color);\r
continue;\r
}\r
\r
- lastrow = (int)(row*sampleRow);\r
+\r
lastcol = (int)(col*sampleCol);\r
\r
- if(av.alignment.getSequenceAt(lastrow).getLength()>lastcol)\r
+ if (seq.getLength() > lastcol)\r
{\r
- color = sr.getResidueBoxColour(\r
- av.alignment.getSequenceAt(lastrow), lastcol);\r
+ color = sr.getResidueBoxColour(\r
+ seq, lastcol).getRGB();\r
\r
- if(av.showSequenceFeatures)\r
- color = fr.findFeatureColour(color, av.alignment.getSequenceAt(lastrow),\r
- lastcol);\r
+ if (av.showSequenceFeatures)\r
+ color = fr.findFeatureColour(color, seq, lastcol);\r
+ }\r
+ else\r
+ {\r
+ color = -1; //White\r
+ }\r
\r
+ if(hiddenRow ||\r
+ (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))\r
+ {\r
+ color = new Color(color).darker().darker().getRGB();\r
}\r
\r
- miniMe.setRGB(col,row,color.getRGB());\r
\r
- if (av.conservation != null)\r
+ miniMe.setRGB(col,row,color);\r
+\r
+\r
+ }\r
+ }\r
+\r
+ if (av.conservation != null)\r
+ {\r
+ for (col = 0; col < width; col++)\r
+ {\r
+ lastcol = (int) (col * sampleCol);\r
{\r
mg.translate(col, sequencesHeight);\r
ap.annotationPanel.drawGraph(mg, av.conservation,\r
graphHeight,\r
(int) (col * sampleCol),\r
(int) (col * sampleCol) + 1);\r
- mg.translate(-col, -sequencesHeight);\r
+ mg.translate( -col, -sequencesHeight);\r
}\r
}\r
}\r
-\r
System.gc();\r
\r
resizing = false;\r
public void setBoxPosition()\r
{\r
int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();\r
- int fullsizeHeight = av.alignment.getHeight() * av.getCharHeight();\r
+ int fullsizeHeight = (av.alignment.getHeight()\r
+ +av.alignment.getHiddenSequences().getSize()) * av.getCharHeight();\r
+\r
+ int startRes = av.getStartRes();\r
+ int endRes = av.getEndRes();\r
+\r
+ if(av.hasHiddenColumns)\r
+ {\r
+ startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);\r
+ endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);\r
+ }\r
+\r
+ int startSeq = av.startSeq;\r
+ int endSeq = av.endSeq;\r
+\r
+ if (av.hasHiddenRows)\r
+ {\r
+ startSeq =\r
+ av.alignment.getHiddenSequences().adjustForHiddenSeqs(startSeq);\r
+\r
+ endSeq =\r
+ av.alignment.getHiddenSequences().adjustForHiddenSeqs(endSeq);\r
+\r
+ }\r
+\r
\r
scalew = (float) width / (float) fullsizeWidth;\r
scaleh = (float) sequencesHeight / (float) fullsizeHeight;\r
\r
- boxX = (int) (av.getStartRes() * av.getCharWidth() * scalew);\r
- boxY = (int) (av.getStartSeq() * av.getCharHeight() * scaleh);\r
- boxWidth = (int) ((av.getEndRes() - av.getStartRes() + 1) * av.getCharWidth() * scalew);\r
- boxHeight = (int) (av.getEndSeq() * av.getCharHeight() * scaleh) -\r
- boxY;\r
+ boxX = (int) (startRes * av.getCharWidth() * scalew);\r
+ boxY = (int) (startSeq * av.getCharHeight() * scaleh);\r
+\r
+\r
+\r
+ if(av.hasHiddenColumns)\r
+ boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);\r
+ else\r
+ boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);\r
+\r
+\r
+ boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);\r
+\r
+\r
repaint();\r
}\r
\r
git://source.jalview.org / jalview.git / blobdiff