+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\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
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
-import javax.swing.*;\r
+import java.awt.*;\r
import java.awt.event.*;\r
import java.awt.image.*;\r
-import java.awt.*;\r
+import javax.swing.*;\r
\r
-public class OverviewPanel extends JPanel\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class OverviewPanel\r
+ extends JPanel implements Runnable\r
{\r
BufferedImage miniMe;\r
AlignViewport av;\r
AlignmentPanel ap;\r
float scalew = 1f;\r
float scaleh = 1f;\r
-\r
- int sequencesWidth, sequencesHeight;\r
- int graphHeight=30;\r
- int boxX=-1, boxY=-1, boxWidth=-1, boxHeight=-1;\r
-\r
- public OverviewPanel(AlignmentPanel ap, AlignViewport av)\r
+ int width;\r
+ int sequencesHeight;\r
+ int graphHeight = 20;\r
+ int boxX = -1;\r
+ int boxY = -1;\r
+ int boxWidth = -1;\r
+ int boxHeight = -1;\r
+ boolean resizing = false;\r
+\r
+ // Can set different properties in this seqCanvas than\r
+ // main visible SeqCanvas\r
+ SequenceRenderer sr;\r
+ FeatureRenderer fr;\r
+\r
+ /**\r
+ * Creates a new OverviewPanel object.\r
+ *\r
+ * @param ap DOCUMENT ME!\r
+ */\r
+ public OverviewPanel(AlignmentPanel ap)\r
{\r
- this.av = av;\r
+ this.av = ap.av;\r
this.ap = ap;\r
+ setLayout(null);\r
+\r
+ sr = new SequenceRenderer(av);\r
+ sr.renderGaps = false;\r
+ sr.forOverview = true;\r
+ fr = new FeatureRenderer(ap);\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.conservation == null)\r
+ {\r
+ graphHeight = 0;\r
+ }\r
\r
- float initialScale = (float)av.getAlignment().getWidth()/(float)av.getAlignment().getHeight();\r
- if(av.getAlignment().getWidth() > av.getAlignment().getHeight())\r
+ if (av.alignment.getWidth() > av.alignment.getHeight())\r
{\r
// wider\r
- sequencesWidth = 400;\r
- sequencesHeight = (int)(400f/initialScale);\r
+ width = 400;\r
+ sequencesHeight = (int) (400f / initialScale);\r
+ if (sequencesHeight < 40)\r
+ {\r
+ sequencesHeight = 40;\r
+ }\r
}\r
else\r
{\r
// taller\r
- sequencesWidth = (int)(400f*initialScale);\r
+ width = (int) (400f * initialScale);\r
sequencesHeight = 300;\r
- }\r
\r
-\r
-\r
- setSize(sequencesWidth, sequencesHeight+graphHeight);\r
- setLayout(null);\r
-\r
- updateOverviewImage();\r
+ if (width < 120)\r
+ {\r
+ width = 120;\r
+ }\r
+ }\r
\r
addComponentListener(new ComponentAdapter()\r
- {\r
-\r
- public void componentResized(ComponentEvent evt)\r
- {\r
- if( getWidth()!=sequencesWidth || getHeight()!=sequencesHeight+graphHeight)\r
- updateOverviewImage();\r
- }\r
- });\r
-\r
+ {\r
+ public void componentResized(ComponentEvent evt)\r
+ {\r
+ if ( (getWidth() != width) ||\r
+ (getHeight() != (sequencesHeight + graphHeight)))\r
+ {\r
+ updateOverviewImage();\r
+ }\r
+ }\r
+ });\r
\r
addMouseMotionListener(new MouseMotionAdapter()\r
- {\r
- public void mouseDragged(MouseEvent evt)\r
- { doMouseDragged(evt);}\r
- });\r
+ {\r
+ public void mouseDragged(MouseEvent evt)\r
+ {\r
+ if (!av.wrapAlignment)\r
+ {\r
+ boxX = evt.getX();\r
+ boxY = evt.getY();\r
+ checkValid();\r
+ }\r
+ }\r
+ });\r
\r
addMouseListener(new MouseAdapter()\r
{\r
public void mousePressed(MouseEvent evt)\r
- { doMousePressed(evt);}\r
- public void mouseReleased(MouseEvent evt)\r
- { doMouseReleased(evt);}\r
+ {\r
+ if (!av.wrapAlignment)\r
+ {\r
+ boxX = evt.getX();\r
+ boxY = evt.getY();\r
+ checkValid();\r
+ }\r
+ }\r
});\r
\r
+ updateOverviewImage();\r
}\r
\r
- public void doMousePressed(MouseEvent evt)\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ void checkValid()\r
{\r
- checkValid(evt.getX(), evt.getY());\r
- repaint();\r
- }\r
+ if (boxY < 0)\r
+ {\r
+ boxY = 0;\r
+ }\r
\r
- public void doMouseReleased(MouseEvent evt)\r
- {\r
- int x = evt.getX();\r
- int y = evt.getY();\r
- checkValid(x, y);\r
- ap.setScrollValues( (int)(x/scalew/av.getCharWidth()), (int)(y/scaleh/av.getCharHeight()) );\r
- }\r
+ if (boxY > (sequencesHeight - boxHeight))\r
+ {\r
+ boxY = sequencesHeight - boxHeight + 1;\r
+ }\r
\r
- public void doMouseDragged(MouseEvent evt)\r
- {\r
- int x = evt.getX();\r
- int y = evt.getY();\r
- checkValid(x, y);\r
- ap.setScrollValues( (int)(x/scalew/av.getCharWidth()), (int)(y/scaleh/av.getCharHeight()) );\r
- repaint();\r
- }\r
+ if (boxX < 0)\r
+ {\r
+ boxX = 0;\r
+ }\r
\r
- void checkValid(int x, int y)\r
- {\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
- if (y < 0)\r
- y = 0;\r
- if (y > sequencesHeight - boxHeight)\r
- y = sequencesHeight- boxHeight;\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
- if (x < 0)\r
- x = 0;\r
+ col = av.getColumnSelection().findColumnPosition(col);\r
+ }\r
\r
- if (x > sequencesWidth - boxWidth)\r
- x = sequencesWidth - boxWidth;\r
+ if (av.hasHiddenRows)\r
+ {\r
+ row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(row);\r
+ }\r
+\r
+ ap.setScrollValues(col, row);\r
\r
- boxX = x;\r
- boxY = y;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
public void updateOverviewImage()\r
{\r
- miniMe = null;\r
- setPreferredSize (new Dimension(sequencesWidth, sequencesHeight+graphHeight));\r
- sequencesWidth=getWidth();\r
- sequencesHeight=this.getHeight()-graphHeight;\r
+ if (resizing)\r
+ {\r
+ resizeAgain = true;\r
+ return;\r
+ }\r
+\r
+ resizing = true;\r
+\r
+ if ( (getWidth() > 0) && (getHeight() > 0))\r
+ {\r
+ width = getWidth();\r
+ sequencesHeight = getHeight() - graphHeight;\r
+ }\r
+\r
+ setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));\r
\r
+ Thread thread = new Thread(this);\r
+ thread.start();\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
\r
- int fullsizeWidth = (int)(av.getAlignment().getWidth()*av.getCharWidth());\r
- int fullsizeHeight = av.getAlignment().getHeight()*av.getCharHeight();\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void run()\r
+ {\r
+ miniMe = null;\r
\r
+ if (av.showSequenceFeatures)\r
+ {\r
+ fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());\r
+ }\r
\r
- BufferedImage fullSize = new BufferedImage(fullsizeWidth,\r
- fullsizeHeight,\r
- BufferedImage.TYPE_INT_RGB);\r
+ int alwidth = av.alignment.getWidth();\r
+ int alheight = av.alignment.getHeight()\r
+ + av.alignment.getHiddenSequences().getSize();\r
\r
- BufferedImage consensus = new BufferedImage(fullsizeWidth,\r
- 80,\r
- BufferedImage.TYPE_INT_RGB);\r
+ setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));\r
\r
+ int fullsizeWidth = alwidth * av.getCharWidth();\r
+ int fullsizeHeight = alheight * av.getCharHeight();\r
\r
- Graphics g = fullSize.getGraphics();\r
- ap.seqPanel.seqCanvas.drawPanel(g,0,av.getAlignment().getWidth(),0,av.getAlignment().getHeight(),0,0,0);\r
+ scalew = (float) width / (float) fullsizeWidth;\r
+ scaleh = (float) sequencesHeight / (float) fullsizeHeight;\r
\r
- g = consensus.getGraphics();\r
- ap.scorePanel.drawScorePanel(g, fullsizeWidth, 0, av.getAlignment().getWidth());\r
+ miniMe = new BufferedImage(width, sequencesHeight + graphHeight,\r
+ BufferedImage.TYPE_INT_RGB);\r
\r
- try{\r
- miniMe = new BufferedImage(sequencesWidth, sequencesHeight + graphHeight,\r
- BufferedImage.TYPE_INT_RGB);\r
- Graphics mg = miniMe.getGraphics();\r
+ Graphics mg = miniMe.getGraphics();\r
+ mg.setColor(Color.orange);\r
+ mg.fillRect(0, 0, width, miniMe.getHeight());\r
\r
- mg.drawImage(fullSize, 0, 0, sequencesWidth, sequencesHeight, 0, 0,\r
- fullsizeWidth, fullsizeHeight, this);\r
- mg.drawImage(consensus, 0, sequencesHeight, sequencesWidth,\r
- sequencesHeight + graphHeight, 0, 0, fullsizeWidth, 60, this);\r
+ float sampleCol = (float) alwidth / (float) width;\r
+ float sampleRow = (float) alheight / (float) sequencesHeight;\r
\r
- scalew = (float) sequencesWidth / (float) fullsizeWidth;\r
- scaleh = (float) sequencesHeight / (float) fullsizeHeight;\r
+ int lastcol = -1, lastrow = -1;\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
+ 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(\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 (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 &&\r
+ (int) (row * sampleRow) == lastrow)\r
+ {\r
+ miniMe.setRGB(col, row, color);\r
+ continue;\r
+ }\r
+\r
+ lastcol = (int) (col * sampleCol);\r
+\r
+ if (seq.getLength() > lastcol)\r
+ {\r
+ color = sr.getResidueBoxColour(\r
+ seq, lastcol).getRGB();\r
+\r
+ if (av.showSequenceFeatures)\r
+ {\r
+ color = fr.findFeatureColour(color, seq, lastcol);\r
+ }\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);\r
+\r
+ }\r
+ }\r
\r
- setBoxPosition();\r
- }catch(Exception ex)\r
- {// most likely the frame size is zero\r
- miniMe = null;\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
+ {\r
+ resizeAgain = false;\r
+ updateOverviewImage();\r
+ }\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
public void setBoxPosition()\r
{\r
- boxX = (int) (av.getStartRes() * av.getCharWidth() * scalew);\r
- boxY = (int) (av.getStartSeq() * av.getCharHeight() * scaleh);\r
- boxWidth = (int) (av.getEndRes() * av.getCharWidth() * scalew) - boxX;\r
- boxHeight = (int) (av.getEndSeq() * av.getCharHeight() * scaleh) - boxY;\r
- repaint();\r
+ int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();\r
+ int fullsizeHeight = (av.alignment.getHeight()\r
+ + av.alignment.getHiddenSequences().getSize()) *\r
+ av.getCharHeight();\r
\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) (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
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ */\r
public void paintComponent(Graphics g)\r
{\r
- if(miniMe!=null)\r
- g.drawImage(miniMe, 0,0,this);\r
+ if(resizing)\r
+ {\r
+ g.setColor(Color.white);\r
+ g.fillRect(0,0,getWidth(),getHeight());\r
+ }\r
+ else if (miniMe != null)\r
+ {\r
+ g.drawImage(miniMe, 0, 0, this);\r
+ }\r
\r
g.setColor(Color.red);\r
-\r
g.drawRect(boxX, boxY, boxWidth, boxHeight);\r
- g.drawRect(boxX+1, boxY+1, boxWidth-2, boxHeight-2);\r
- }\r
+ g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);\r
\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff