/*\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
extends Panel implements Runnable, MouseMotionListener, MouseListener\r
{\r
Image miniMe;\r
+ Image offscreen;\r
AlignViewport av;\r
AlignmentPanel ap;\r
float scalew = 1f;\r
SequenceRenderer sr;\r
FeatureRenderer fr;\r
\r
-\r
Frame nullFrame;\r
\r
public OverviewPanel(AlignmentPanel ap)\r
nullFrame = new Frame();\r
nullFrame.addNotify();\r
\r
-\r
sr = new SequenceRenderer(av);\r
sr.graphics = nullFrame.getGraphics();\r
- sr.renderGaps( false );\r
+ sr.renderGaps = false;\r
+ sr.forOverview = true;\r
fr = new FeatureRenderer(av);\r
- fr.drawText = false;\r
-\r
-\r
+ fr.overview = true;\r
\r
// scale the initial size of overviewpanel to shape of alignment\r
float initialScale = (float) av.alignment.getWidth() /\r
(float) av.alignment.getHeight();\r
\r
- if(av.vconsensus==null)\r
- graphHeight = 0;\r
+ if (av.hconsensus == null)\r
+ {\r
+ graphHeight = 0;\r
+ }\r
\r
if (av.alignment.getWidth() > av.alignment.getHeight())\r
{\r
// wider\r
width = 400;\r
sequencesHeight = (int) (400f / initialScale);\r
- if(sequencesHeight<40)\r
- sequencesHeight = 40;\r
+ if (sequencesHeight < 40)\r
+ {\r
+ sequencesHeight = 40;\r
+ }\r
}\r
else\r
{\r
\r
}\r
\r
-\r
public void mouseEntered(MouseEvent evt)\r
{}\r
+\r
public void mouseExited(MouseEvent evt)\r
{}\r
+\r
public void mouseClicked(MouseEvent evt)\r
{}\r
+\r
public void mouseMoved(MouseEvent evt)\r
{}\r
+\r
public void mousePressed(MouseEvent evt)\r
{\r
boxX = evt.getX();\r
boxY = evt.getY();\r
-\r
checkValid();\r
- repaint();\r
}\r
\r
public void mouseReleased(MouseEvent evt)\r
boxX = evt.getX();\r
boxY = evt.getY();\r
checkValid();\r
- ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),\r
- (int) (boxY / scaleh / av.getCharHeight()));\r
}\r
\r
public void mouseDragged(MouseEvent evt)\r
boxX = evt.getX();\r
boxY = evt.getY();\r
checkValid();\r
- ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),\r
- (int) (boxY / scaleh / av.getCharHeight()));\r
-\r
- repaint();\r
- ap.repaint();\r
}\r
\r
void checkValid()\r
boxY = 0;\r
}\r
\r
- if (boxY > sequencesHeight - boxHeight)\r
+ if (boxY > (sequencesHeight - boxHeight))\r
{\r
boxY = sequencesHeight - boxHeight + 1;\r
}\r
boxX = 0;\r
}\r
\r
- if (boxX > width - boxWidth)\r
+ if (boxX > (width - boxWidth))\r
{\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
+ ap.paintAlignment(false);\r
}\r
\r
/**\r
{\r
if (resizing)\r
{\r
- resizeAgain = true;\r
- return;\r
+ resizeAgain = true;\r
+ return;\r
}\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
- }\r
-\r
+ {\r
+ fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().\r
+ featureGroups;\r
+ fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().\r
+ featureColours;\r
+ }\r
\r
resizing = true;\r
\r
sequencesHeight = getSize().height - graphHeight;\r
}\r
setSize(new Dimension(width, sequencesHeight + graphHeight));\r
- setBoxPosition();\r
\r
Thread thread = new Thread(this);\r
thread.start();\r
- repaint();\r
+ repaint();\r
}\r
\r
// This is set true if the user resizes whilst\r
// the overview is being calculated\r
- boolean resizeAgain = false;\r
+ boolean resizeAgain = false;\r
\r
public void run()\r
{\r
int alwidth = av.alignment.getWidth();\r
int alheight = av.alignment.getHeight();\r
\r
+ if (av.showSequenceFeatures)\r
+ {\r
+ fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());\r
+ }\r
+\r
if (getSize().width > 0 && getSize().height > 0)\r
{\r
width = getSize().width;\r
scaleh = (float) sequencesHeight / (float) fullsizeHeight;\r
\r
miniMe = nullFrame.createImage(width, sequencesHeight + graphHeight);\r
+ offscreen = nullFrame.createImage(width, sequencesHeight + graphHeight);\r
\r
Graphics mg = miniMe.getGraphics();\r
float sampleCol = (float) alwidth / (float) width;\r
float sampleRow = (float) alheight / (float) sequencesHeight;\r
\r
- int lastcol=-1, lastrow=-1;\r
+ int lastcol = 0, lastrow = 0;\r
+ int xstart = 0, ystart = 0;\r
Color color = Color.yellow;\r
- int row, col;\r
- for (col = 0; col < width; col++)\r
+ int row, col, sameRow = 0, sameCol = 0;\r
+ jalview.datamodel.SequenceI seq;\r
+ boolean hiddenRow = false;\r
+ for (row = 0; row <= sequencesHeight; row++)\r
{\r
- for (row = 0; row < sequencesHeight; row++)\r
+ if ( (int) (row * sampleRow) == lastrow)\r
+ {\r
+ sameRow++;\r
+ continue;\r
+ }\r
+\r
+ hiddenRow = false;\r
+ if (av.hasHiddenRows)\r
{\r
- if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)\r
+ seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);\r
+ if (seq == null)\r
{\r
- mg.drawLine(col, row, col, row);\r
- continue;\r
+ int index =\r
+ av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(\r
+ lastrow);\r
+\r
+ seq = av.alignment.getSequenceAt(index);\r
}\r
+ else\r
+ {\r
+ hiddenRow = true;\r
+ }\r
+ }\r
+ else\r
+ {\r
+ seq = av.alignment.getSequenceAt(lastrow);\r
+ }\r
\r
- if (av.conservation != null)\r
+ for (col = 0; col < width; col++)\r
+ {\r
+ if ( (int) (col * sampleCol) == lastcol &&\r
+ (int) (row * sampleRow) == lastrow)\r
{\r
- mg.translate(col, sequencesHeight);\r
- ap.annotationPanel.drawGraph(mg, av.conservation,\r
- (int) (sampleCol) + 1,\r
- graphHeight,\r
- (int) (col * sampleCol),\r
- (int) (col * sampleCol) + 1);\r
- mg.translate( -col, -sequencesHeight);\r
+ sameCol++;\r
+ continue;\r
}\r
\r
- lastrow = (int)(row*sampleRow);\r
- lastcol = (int)(col*sampleCol);\r
+ lastcol = (int) (col * sampleCol);\r
\r
- if(av.alignment.getSequenceAt(lastrow).getLength()>lastcol)\r
+ if (seq.getLength() > lastcol)\r
{\r
- color = sr.findSequenceColour(av.alignment.getSequenceAt(lastrow), lastcol);\r
-\r
+ color = sr.getResidueBoxColour(\r
+ seq, lastcol);\r
\r
if (av.showSequenceFeatures)\r
- color = fr.findFeatureColour(color,\r
- av.alignment.getSequenceAt(lastrow),\r
- lastcol);\r
+ {\r
+ color = fr.findFeatureColour(color, seq, lastcol);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ color = Color.white; //White\r
+ }\r
+\r
+ if (hiddenRow ||\r
+ (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))\r
+ {\r
+ color = color.darker().darker();\r
}\r
\r
mg.setColor(color);\r
- mg.drawLine(col,row,col,row);\r
+ if (sameCol == 1 && sameRow == 1)\r
+ {\r
+ mg.drawLine(xstart, ystart, xstart, ystart);\r
+ }\r
+ else\r
+ {\r
+ mg.fillRect(xstart, ystart, sameCol, sameRow);\r
+ }\r
\r
+ xstart = col;\r
+ sameCol = 1;\r
}\r
+ lastrow = (int) (row * sampleRow);\r
+ ystart = row;\r
+ sameRow = 1;\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
+ (int) (sampleCol) + 1,\r
+ graphHeight,\r
+ (int) (col * sampleCol),\r
+ (int) (col * sampleCol) + 1);\r
+ mg.translate( -col, -sequencesHeight);\r
+ }\r
+ }\r
+ }\r
System.gc();\r
\r
resizing = false;\r
\r
setBoxPosition();\r
\r
- if(resizeAgain)\r
+ if (resizeAgain)\r
{\r
resizeAgain = false;\r
updateOverviewImage();\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()) *\r
+ 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
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) *\r
- av.getCharWidth() * scalew);\r
- boxHeight = (int) (av.getEndSeq() * av.getCharHeight() * scaleh) - boxY;\r
+ boxX = (int) (startRes * av.getCharWidth() * scalew);\r
+ boxY = (int) (startSeq * av.getCharHeight() * scaleh);\r
+\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);\r
+ }\r
+ else\r
+ {\r
+ boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);\r
+ }\r
+\r
+ boxHeight = (int) ( (endSeq - startSeq) * av.getCharHeight() * scaleh);\r
+\r
repaint();\r
}\r
\r
\r
public void paint(Graphics g)\r
{\r
+ Graphics og = offscreen.getGraphics();\r
if (miniMe != null)\r
{\r
- g.drawImage(miniMe, 0, 0, this);\r
- }\r
- else\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, getSize().width, getSize().height);\r
- g.setColor(Color.black);\r
- g.setFont(new Font("Verdana", Font.BOLD, 15));\r
- g.drawString("Recalculating", 5, sequencesHeight / 2);\r
- g.drawString("Overview.....", 5, (sequencesHeight / 2) + 20);\r
+ og.drawImage(miniMe, 0, 0, this);\r
+ og.setColor(Color.red);\r
+ og.drawRect(boxX, boxY, boxWidth, boxHeight);\r
+ og.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);\r
+ g.drawImage(offscreen, 0, 0, this);\r
}\r
-\r
- g.setColor(Color.red);\r
- g.drawRect(boxX, boxY, boxWidth, boxHeight);\r
- g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);\r
}\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff