-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 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
-\r
-package jalview.appletgui;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-public class OverviewPanel\r
- extends Panel implements Runnable, MouseMotionListener, MouseListener\r
-{\r
- Image miniMe;\r
- AlignViewport av;\r
- AlignmentPanel ap;\r
- float scalew = 1f;\r
- float scaleh = 1f;\r
-\r
- public int width, sequencesHeight;\r
- int graphHeight = 20;\r
- int boxX = -1, boxY = -1, boxWidth = -1, boxHeight = -1;\r
-\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
- Frame nullFrame;\r
-\r
- public OverviewPanel(AlignmentPanel ap)\r
- {\r
- this.av = ap.av;\r
- this.ap = ap;\r
- setLayout(null);\r
- nullFrame = new Frame();\r
- nullFrame.addNotify();\r
-\r
-\r
- sr = new SequenceRenderer(av);\r
- sr.graphics = nullFrame.getGraphics();\r
- sr.renderGaps( false );\r
- //fr = new FeatureRenderer(av);\r
- //fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;\r
- //fr.featuresDisplayed = ap.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed;\r
-\r
-\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
-\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
- }\r
- else\r
- {\r
- // taller\r
- width = (int) (400f * initialScale);\r
- sequencesHeight = 300;\r
- if (width < 120)\r
- {\r
- width = 120;\r
- }\r
- }\r
-\r
- setSize(new Dimension(width, sequencesHeight + graphHeight));\r
- addComponentListener(new ComponentAdapter()\r
- {\r
-\r
- public void componentResized(ComponentEvent evt)\r
- {\r
- if (getSize().width != width ||\r
- getSize().height != sequencesHeight + graphHeight)\r
- {\r
- updateOverviewImage();\r
- }\r
- }\r
- });\r
-\r
- addMouseMotionListener(this);\r
-\r
- addMouseListener(this);\r
-\r
- updateOverviewImage();\r
-\r
- }\r
-\r
-\r
- public void mouseEntered(MouseEvent evt)\r
- {}\r
- public void mouseExited(MouseEvent evt)\r
- {}\r
- public void mouseClicked(MouseEvent evt)\r
- {}\r
- public void mouseMoved(MouseEvent evt)\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
- {\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
- {\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
- {\r
- if (boxY < 0)\r
- {\r
- boxY = 0;\r
- }\r
-\r
- if (boxY > sequencesHeight - boxHeight)\r
- {\r
- boxY = sequencesHeight - boxHeight + 1;\r
- }\r
-\r
- if (boxX < 0)\r
- {\r
- boxX = 0;\r
- }\r
-\r
- if (boxX > width - boxWidth)\r
- {\r
- boxX = width - boxWidth;\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void updateOverviewImage()\r
- {\r
- if (resizing)\r
- {\r
- resizeAgain = true;\r
- return;\r
- }\r
-\r
- resizing = true;\r
-\r
- if ( (getSize().width > 0) && (getSize().height > 0))\r
- {\r
- width = getSize().width;\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
- }\r
-\r
- // This is set true if the user resizes whilst\r
- // the overview is being calculated\r
- boolean resizeAgain = false;\r
-\r
- public void run()\r
- {\r
- miniMe = null;\r
- int alwidth = av.alignment.getWidth();\r
- int alheight = av.alignment.getHeight();\r
-\r
- if (getSize().width > 0 && getSize().height > 0)\r
- {\r
- width = getSize().width;\r
- sequencesHeight = getSize().height - graphHeight;\r
- }\r
-\r
- setSize(new Dimension(width, sequencesHeight + graphHeight));\r
-\r
- int fullsizeWidth = alwidth * av.getCharWidth();\r
- int fullsizeHeight = alheight * av.getCharHeight();\r
-\r
- scalew = (float) width / (float) fullsizeWidth;\r
- scaleh = (float) sequencesHeight / (float) fullsizeHeight;\r
-\r
- miniMe = 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
- Color color = Color.white;\r
- for (int col = 0; col < width; col++)\r
- {\r
- for (int row = 0; row < sequencesHeight; row++)\r
- {\r
- if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)\r
- {\r
- mg.setColor(color);\r
- mg.fillRect(col,row,1,1);\r
- continue;\r
- }\r
-\r
- lastrow = (int)(row*sampleRow);\r
- lastcol = (int)(col*sampleCol);\r
-\r
- color = sr.findSequenceColour(av.alignment.getSequenceAt(lastrow), lastcol);\r
-\r
- mg.setColor(color);\r
- mg.fillRect(col,row,1,1);\r
-\r
- if (av.conservation != null)\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
-\r
- System.gc();\r
-\r
- resizing = false;\r
-\r
- setBoxPosition();\r
-\r
- if(resizeAgain)\r
- {\r
- resizeAgain = false;\r
- updateOverviewImage();\r
- }\r
- }\r
-\r
- public void setBoxPosition()\r
- {\r
- int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();\r
- int fullsizeHeight = av.alignment.getHeight() * av.getCharHeight();\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
- repaint();\r
- }\r
-\r
- public void update(Graphics g)\r
- {\r
- paint(g);\r
- }\r
-\r
- public void paint(Graphics g)\r
- {\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
- }\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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.appletgui;
+
+import java.awt.*;
+import java.awt.event.*;
+
+public class OverviewPanel extends Panel implements Runnable,
+ MouseMotionListener, MouseListener
+{
+ Image miniMe;
+
+ Image offscreen;
+
+ AlignViewport av;
+
+ AlignmentPanel ap;
+
+ float scalew = 1f;
+
+ float scaleh = 1f;
+
+ public int width, sequencesHeight;
+
+ int graphHeight = 20;
+
+ int boxX = -1, boxY = -1, boxWidth = -1, boxHeight = -1;
+
+ boolean resizing = false;
+
+ // Can set different properties in this seqCanvas than
+ // main visible SeqCanvas
+ SequenceRenderer sr;
+
+ FeatureRenderer fr;
+
+ Frame nullFrame;
+
+ public OverviewPanel(AlignmentPanel ap)
+ {
+ this.av = ap.av;
+ this.ap = ap;
+ setLayout(null);
+ nullFrame = new Frame();
+ nullFrame.addNotify();
+
+ sr = new SequenceRenderer(av);
+ sr.graphics = nullFrame.getGraphics();
+ sr.renderGaps = false;
+ sr.forOverview = true;
+ fr = new FeatureRenderer(av);
+ fr.overview = true;
+
+ // scale the initial size of overviewpanel to shape of alignment
+ float initialScale = (float) av.alignment.getWidth()
+ / (float) av.alignment.getHeight();
+
+ if (av.hconsensus == null)
+ {
+ graphHeight = 0;
+ }
+
+ if (av.alignment.getWidth() > av.alignment.getHeight())
+ {
+ // wider
+ width = 400;
+ sequencesHeight = (int) (400f / initialScale);
+ if (sequencesHeight < 40)
+ {
+ sequencesHeight = 40;
+ }
+ }
+ else
+ {
+ // taller
+ width = (int) (400f * initialScale);
+ sequencesHeight = 300;
+ if (width < 120)
+ {
+ width = 120;
+ }
+ }
+
+ setSize(new Dimension(width, sequencesHeight + graphHeight));
+ addComponentListener(new ComponentAdapter()
+ {
+
+ public void componentResized(ComponentEvent evt)
+ {
+ if (getSize().width != width
+ || getSize().height != sequencesHeight + graphHeight)
+ {
+ updateOverviewImage();
+ }
+ }
+ });
+
+ addMouseMotionListener(this);
+
+ addMouseListener(this);
+
+ updateOverviewImage();
+
+ }
+
+ public void mouseEntered(MouseEvent evt)
+ {
+ }
+
+ public void mouseExited(MouseEvent evt)
+ {
+ }
+
+ public void mouseClicked(MouseEvent evt)
+ {
+ }
+
+ public void mouseMoved(MouseEvent evt)
+ {
+ }
+
+ public void mousePressed(MouseEvent evt)
+ {
+ boxX = evt.getX();
+ boxY = evt.getY();
+ checkValid();
+ }
+
+ public void mouseReleased(MouseEvent evt)
+ {
+ boxX = evt.getX();
+ boxY = evt.getY();
+ checkValid();
+ }
+
+ public void mouseDragged(MouseEvent evt)
+ {
+ boxX = evt.getX();
+ boxY = evt.getY();
+ checkValid();
+ }
+
+ void checkValid()
+ {
+ if (boxY < 0)
+ {
+ boxY = 0;
+ }
+
+ if (boxY > (sequencesHeight - boxHeight))
+ {
+ boxY = sequencesHeight - boxHeight + 1;
+ }
+
+ if (boxX < 0)
+ {
+ boxX = 0;
+ }
+
+ if (boxX > (width - boxWidth))
+ {
+ if (av.hasHiddenColumns)
+ {
+ // Try smallest possible box
+ boxWidth = (int) ((av.endRes - av.startRes + 1) * av.getCharWidth() * scalew);
+ }
+ boxX = width - boxWidth;
+ }
+
+ int col = (int) (boxX / scalew / av.getCharWidth());
+ int row = (int) (boxY / scaleh / av.getCharHeight());
+
+ if (av.hasHiddenColumns)
+ {
+ if (!av.getColumnSelection().isVisible(col))
+ {
+ return;
+ }
+
+ col = av.getColumnSelection().findColumnPosition(col);
+ }
+
+ if (av.hasHiddenRows)
+ {
+ row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(
+ row);
+ }
+
+ ap.setScrollValues(col, row);
+ ap.paintAlignment(false);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void updateOverviewImage()
+ {
+ if (resizing)
+ {
+ resizeAgain = true;
+ return;
+ }
+
+ if (av.showSequenceFeatures)
+ {
+ fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;
+ fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
+ }
+
+ resizing = true;
+
+ if ((getSize().width > 0) && (getSize().height > 0))
+ {
+ width = getSize().width;
+ sequencesHeight = getSize().height - graphHeight;
+ }
+ setSize(new Dimension(width, sequencesHeight + graphHeight));
+
+ Thread thread = new Thread(this);
+ thread.start();
+ repaint();
+ }
+
+ // This is set true if the user resizes whilst
+ // the overview is being calculated
+ boolean resizeAgain = false;
+
+ public void run()
+ {
+ miniMe = null;
+ int alwidth = av.alignment.getWidth();
+ int alheight = av.alignment.getHeight();
+
+ if (av.showSequenceFeatures)
+ {
+ fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
+ }
+
+ if (getSize().width > 0 && getSize().height > 0)
+ {
+ width = getSize().width;
+ sequencesHeight = getSize().height - graphHeight;
+ }
+
+ setSize(new Dimension(width, sequencesHeight + graphHeight));
+
+ int fullsizeWidth = alwidth * av.getCharWidth();
+ int fullsizeHeight = alheight * av.getCharHeight();
+
+ scalew = (float) width / (float) fullsizeWidth;
+ scaleh = (float) sequencesHeight / (float) fullsizeHeight;
+
+ miniMe = nullFrame.createImage(width, sequencesHeight + graphHeight);
+ offscreen = nullFrame.createImage(width, sequencesHeight + graphHeight);
+
+ Graphics mg = miniMe.getGraphics();
+ float sampleCol = (float) alwidth / (float) width;
+ float sampleRow = (float) alheight / (float) sequencesHeight;
+
+ int lastcol = 0, lastrow = 0;
+ int xstart = 0, ystart = 0;
+ Color color = Color.yellow;
+ int row, col, sameRow = 0, sameCol = 0;
+ jalview.datamodel.SequenceI seq;
+ boolean hiddenRow = false;
+ for (row = 0; row <= sequencesHeight; row++)
+ {
+ if ((int) (row * sampleRow) == lastrow)
+ {
+ sameRow++;
+ continue;
+ }
+
+ hiddenRow = false;
+ if (av.hasHiddenRows)
+ {
+ seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);
+ if (seq == null)
+ {
+ int index = av.alignment.getHiddenSequences()
+ .findIndexWithoutHiddenSeqs(lastrow);
+
+ seq = av.alignment.getSequenceAt(index);
+ }
+ else
+ {
+ hiddenRow = true;
+ }
+ }
+ else
+ {
+ seq = av.alignment.getSequenceAt(lastrow);
+ }
+
+ for (col = 0; col < width; col++)
+ {
+ if ((int) (col * sampleCol) == lastcol
+ && (int) (row * sampleRow) == lastrow)
+ {
+ sameCol++;
+ continue;
+ }
+
+ lastcol = (int) (col * sampleCol);
+
+ if (seq.getLength() > lastcol)
+ {
+ color = sr.getResidueBoxColour(seq, lastcol);
+
+ if (av.showSequenceFeatures)
+ {
+ color = fr.findFeatureColour(color, seq, lastcol);
+ }
+ }
+ else
+ {
+ color = Color.white; // White
+ }
+
+ if (hiddenRow
+ || (av.hasHiddenColumns && !av.getColumnSelection()
+ .isVisible(lastcol)))
+ {
+ color = color.darker().darker();
+ }
+
+ mg.setColor(color);
+ if (sameCol == 1 && sameRow == 1)
+ {
+ mg.drawLine(xstart, ystart, xstart, ystart);
+ }
+ else
+ {
+ mg.fillRect(xstart, ystart, sameCol, sameRow);
+ }
+
+ xstart = col;
+ sameCol = 1;
+ }
+ lastrow = (int) (row * sampleRow);
+ ystart = row;
+ sameRow = 1;
+ }
+
+ if (av.conservation != null)
+ {
+ for (col = 0; col < width; col++)
+ {
+ lastcol = (int) (col * sampleCol);
+ {
+ mg.translate(col, sequencesHeight);
+ ap.annotationPanel.drawGraph(mg, av.conservation,
+ (int) (sampleCol) + 1, graphHeight,
+ (int) (col * sampleCol), (int) (col * sampleCol) + 1);
+ mg.translate(-col, -sequencesHeight);
+ }
+ }
+ }
+ System.gc();
+
+ resizing = false;
+
+ setBoxPosition();
+
+ if (resizeAgain)
+ {
+ resizeAgain = false;
+ updateOverviewImage();
+ }
+ }
+
+ public void setBoxPosition()
+ {
+ int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();
+ int fullsizeHeight = (av.alignment.getHeight() + av.alignment
+ .getHiddenSequences().getSize()) * av.getCharHeight();
+
+ int startRes = av.getStartRes();
+ int endRes = av.getEndRes();
+
+ if (av.hasHiddenColumns)
+ {
+ startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
+ endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
+ }
+
+ int startSeq = av.startSeq;
+ int endSeq = av.endSeq;
+
+ if (av.hasHiddenRows)
+ {
+ startSeq = av.alignment.getHiddenSequences().adjustForHiddenSeqs(
+ startSeq);
+
+ endSeq = av.alignment.getHiddenSequences()
+ .adjustForHiddenSeqs(endSeq);
+
+ }
+
+ scalew = (float) width / (float) fullsizeWidth;
+ scaleh = (float) sequencesHeight / (float) fullsizeHeight;
+
+ boxX = (int) (startRes * av.getCharWidth() * scalew);
+ boxY = (int) (startSeq * av.getCharHeight() * scaleh);
+
+ if (av.hasHiddenColumns)
+ {
+ boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+ }
+ else
+ {
+ boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+ }
+
+ boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);
+
+ repaint();
+ }
+
+ public void update(Graphics g)
+ {
+ paint(g);
+ }
+
+ public void paint(Graphics g)
+ {
+ Graphics og = offscreen.getGraphics();
+ if (miniMe != null)
+ {
+ og.drawImage(miniMe, 0, 0, this);
+ og.setColor(Color.red);
+ og.drawRect(boxX, boxY, boxWidth, boxHeight);
+ og.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
+ g.drawImage(offscreen, 0, 0, this);
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff