-/*\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
-package jalview.gui;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import java.awt.image.*;\r
-import javax.swing.*;\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
- int width;\r
- int sequencesHeight;\r
- int graphHeight = 30;\r
- int boxX = -1;\r
- int boxY = -1;\r
- int boxWidth = -1;\r
- int boxHeight = -1;\r
- boolean resizing = false;\r
-\r
- public OverviewPanel(AlignmentPanel ap)\r
- {\r
- this.av = ap.av;\r
- this.ap = ap;\r
- setLayout(null);\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.alignment.getWidth() > av.alignment.getHeight())\r
- {\r
- // wider\r
- width = 400;\r
- sequencesHeight = (int) (400f / initialScale);\r
- }\r
- else\r
- {\r
- // taller\r
- width = (int) (400f * initialScale);\r
- sequencesHeight = 300;\r
-\r
- if (width < 120)\r
- {\r
- width = 120;\r
- }\r
- }\r
-\r
- addComponentListener(new ComponentAdapter()\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
- {\r
- doMouseDragged(evt);\r
- }\r
- });\r
-\r
- addMouseListener(new MouseAdapter()\r
- {\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- doMousePressed(evt);\r
- }\r
-\r
- public void mouseReleased(MouseEvent evt)\r
- {\r
- doMouseReleased(evt);\r
- }\r
- });\r
-\r
- updateOverviewImage();\r
- }\r
-\r
- public void doMousePressed(MouseEvent evt)\r
- {\r
- boxX = evt.getX();\r
- boxY = evt.getY();\r
-\r
- checkValid();\r
- repaint();\r
- }\r
-\r
- public void doMouseReleased(MouseEvent evt)\r
- {\r
- boxX = evt.getX();\r
- boxY = evt.getY();\r
- checkValid();\r
-\r
- if (!resizing)\r
- {\r
- ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),\r
- (int) (boxY / scaleh / av.getCharHeight()));\r
- }\r
- }\r
-\r
- public void doMouseDragged(MouseEvent evt)\r
- {\r
- boxX = evt.getX();\r
- boxY = evt.getY();\r
- checkValid();\r
-\r
- if (!resizing)\r
- {\r
- ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),\r
- (int) (boxY / scaleh / av.getCharHeight()));\r
- }\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
- public void updateOverviewImage()\r
- {\r
- if (resizing)\r
- {\r
- return;\r
- }\r
-\r
- resizing = true;\r
-\r
- Thread thread = new Thread(this);\r
- thread.start();\r
- repaint();\r
- }\r
-\r
- public void run()\r
- {\r
- miniMe = null;\r
-\r
- int alwidth = av.alignment.getWidth();\r
- int alheight = av.alignment.getHeight();\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
- 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 = new BufferedImage(width, sequencesHeight + graphHeight,\r
- BufferedImage.TYPE_INT_RGB);\r
-\r
- Graphics mg = miniMe.getGraphics();\r
- BufferedImage consensus = new BufferedImage(fullsizeWidth, 60,\r
- BufferedImage.TYPE_3BYTE_BGR);\r
- Graphics g = consensus.getGraphics();\r
- ap.annotationPanel.drawGraph(g, av.conservation, fullsizeWidth, 60);\r
- mg.drawImage(consensus, 0, sequencesHeight, width,\r
- sequencesHeight + graphHeight, 0, 0, fullsizeWidth, 60, this);\r
-\r
- boolean oldRenderGaps = av.renderGaps;\r
-\r
- try\r
- {\r
- // We'll have to draw the full size alignment in chunks, as an image of the\r
- // whole alignment requires too much memory\r
- // Max size depends on the font size, the following is a\r
- // guess at a size which works\r
- int maxSize = 2000 / av.getFont().getSize();\r
- BufferedImage block;\r
- int blockx = 0;\r
- int blocky = 0;\r
- int blockw = 0;\r
- int blockh = 0;\r
- int eRes = 0;\r
- int eSeq = 0;\r
-\r
- av.setRenderGaps(false);\r
-\r
- for (int sRes = 0, chunkx = 0; sRes < alwidth;\r
- sRes += maxSize, chunkx++)\r
- {\r
- eSeq = 0;\r
- eRes += maxSize;\r
-\r
- if (eRes > alwidth)\r
- {\r
- eRes = alwidth;\r
- }\r
-\r
- for (int sSeq = 0, chunky = 0; sSeq < alheight;\r
- sSeq += maxSize, chunky++)\r
- {\r
- eSeq += maxSize;\r
-\r
- if (eSeq > alheight)\r
- {\r
- eSeq = alheight;\r
- }\r
-\r
- blocky = 0;\r
- blockx = (int) ( (float) sRes / (float) alwidth * width);\r
-\r
- block = new BufferedImage( (eRes - sRes) * av.charWidth,\r
- (eSeq - sSeq) * av.charHeight,\r
- BufferedImage.TYPE_3BYTE_BGR);\r
- g = block.getGraphics();\r
-\r
- ap.seqPanel.seqCanvas.drawPanel(g, sRes, eRes, sSeq, eSeq,\r
- sRes, sSeq, 0);\r
-\r
- blockh = (int) ( (float) (eSeq - sSeq) / (float) alheight *\r
- sequencesHeight) +\r
- 1;\r
- blockw = (int) ( (float) (eRes - sRes) / (float) alwidth * width) +\r
- 1;\r
-\r
- blocky += (int) ( (float) sSeq / (float) alheight * sequencesHeight);\r
-\r
- mg.drawImage(block, blockx, blocky, blockx + blockw,\r
- blocky + blockh, 0, 0, block.getWidth(),\r
- block.getHeight(), this);\r
-\r
- block = null;\r
- }\r
- }\r
- }\r
- catch (OutOfMemoryError error)\r
- {\r
- System.err.println(\r
- "Out of memory when trying to calculate the overview window image!");\r
- }\r
-\r
- av.setRenderGaps(oldRenderGaps);\r
- resizing = false;\r
-\r
- setBoxPosition();\r
- }\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.getStartRes() + 1) *\r
- av.getCharWidth() * scalew);\r
- boxHeight = (int) (av.getEndSeq() * av.getCharHeight() * scaleh) -\r
- boxY;\r
- repaint();\r
- }\r
-\r
- public void paintComponent(Graphics g)\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, getWidth(), getHeight());\r
- g.setColor(Color.black);\r
-\r
- if (resizing)\r
- {\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
- else\r
- {\r
- if (miniMe != null)\r
- {\r
- g.drawImage(miniMe, 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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.renderer.AnnotationRenderer;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Graphics;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseMotionAdapter;
+import java.awt.image.BufferedImage;
+
+import javax.swing.JPanel;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class OverviewPanel extends JPanel implements Runnable
+{
+ BufferedImage miniMe;
+
+ AlignViewport av;
+
+ AlignmentPanel ap;
+
+ final AnnotationRenderer renderer = new AnnotationRenderer();
+
+ float scalew = 1f;
+
+ float scaleh = 1f;
+
+ int width;
+
+ int sequencesHeight;
+
+ int graphHeight = 20;
+
+ int boxX = -1;
+
+ int boxY = -1;
+
+ int boxWidth = -1;
+
+ int boxHeight = -1;
+
+ boolean resizing = false;
+
+ // Can set different properties in this seqCanvas than
+ // main visible SeqCanvas
+ SequenceRenderer sr;
+
+ jalview.renderer.seqfeatures.FeatureRenderer fr;
+
+ /**
+ * Creates a new OverviewPanel object.
+ *
+ * @param ap
+ * DOCUMENT ME!
+ */
+ public OverviewPanel(AlignmentPanel ap)
+ {
+ this.av = ap.av;
+ this.ap = ap;
+ setLayout(null);
+
+ sr = new SequenceRenderer(av);
+ sr.renderGaps = false;
+ sr.forOverview = true;
+ fr = new FeatureRenderer(ap);
+
+ // scale the initial size of overviewpanel to shape of alignment
+ float initialScale = (float) av.getAlignment().getWidth()
+ / (float) av.getAlignment().getHeight();
+
+ if (av.getAlignmentConservationAnnotation() == null)
+ {
+ graphHeight = 0;
+ }
+
+ if (av.getAlignment().getWidth() > av.getAlignment().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;
+ }
+ }
+
+ addComponentListener(new ComponentAdapter()
+ {
+ @Override
+ public void componentResized(ComponentEvent evt)
+ {
+ if ((getWidth() != width)
+ || (getHeight() != (sequencesHeight + graphHeight)))
+ {
+ updateOverviewImage();
+ }
+ }
+ });
+
+ addMouseMotionListener(new MouseMotionAdapter()
+ {
+ @Override
+ public void mouseDragged(MouseEvent evt)
+ {
+ if (!av.getWrapAlignment())
+ {
+ // TODO: feature: jv2.5 detect shift drag and update selection from
+ // it.
+ boxX = evt.getX();
+ boxY = evt.getY();
+ checkValid();
+ }
+ }
+ });
+
+ addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ if (!av.getWrapAlignment())
+ {
+ boxX = evt.getX();
+ boxY = evt.getY();
+ checkValid();
+ }
+ }
+ });
+
+ updateOverviewImage();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ 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.getAlignment().getHiddenSequences()
+ .findIndexWithoutHiddenSeqs(row);
+ }
+
+ ap.setScrollValues(col, row);
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void updateOverviewImage()
+ {
+ if (resizing)
+ {
+ resizeAgain = true;
+ return;
+ }
+
+ resizing = true;
+
+ if ((getWidth() > 0) && (getHeight() > 0))
+ {
+ width = getWidth();
+ sequencesHeight = getHeight() - graphHeight;
+ }
+
+ setPreferredSize(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;
+
+ /**
+ * DOCUMENT ME!
+ */
+ @Override
+ public void run()
+ {
+ miniMe = null;
+
+ if (av.isShowSequenceFeatures())
+ {
+ fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer());
+ }
+
+ int alwidth = av.getAlignment().getWidth();
+ int alheight = av.getAlignment().getHeight()
+ + av.getAlignment().getHiddenSequences().getSize();
+
+ setPreferredSize(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 = new BufferedImage(width, sequencesHeight + graphHeight,
+ BufferedImage.TYPE_INT_RGB);
+
+ Graphics mg = miniMe.getGraphics();
+ mg.setColor(Color.orange);
+ mg.fillRect(0, 0, width, miniMe.getHeight());
+
+ float sampleCol = (float) alwidth / (float) width;
+ float sampleRow = (float) alheight / (float) sequencesHeight;
+
+ int lastcol = -1, lastrow = -1;
+ int color = Color.white.getRGB();
+ int row, col;
+ jalview.datamodel.SequenceI seq;
+ final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
+ .hasHiddenColumns();
+ boolean hiddenRow = false;
+ for (row = 0; row < sequencesHeight; row++)
+ {
+ if ((int) (row * sampleRow) == lastrow)
+ {
+ // No need to recalculate the colours,
+ // Just copy from the row above
+ for (col = 0; col < width; col++)
+ {
+ miniMe.setRGB(col, row, miniMe.getRGB(col, row - 1));
+ }
+ continue;
+ }
+
+ lastrow = (int) (row * sampleRow);
+
+ hiddenRow = false;
+ if (hasHiddenRows)
+ {
+ seq = av.getAlignment().getHiddenSequences()
+ .getHiddenSequence(lastrow);
+ if (seq == null)
+ {
+ int index = av.getAlignment().getHiddenSequences()
+ .findIndexWithoutHiddenSeqs(lastrow);
+
+ seq = av.getAlignment().getSequenceAt(index);
+ }
+ else
+ {
+ hiddenRow = true;
+ }
+ }
+ else
+ {
+ seq = av.getAlignment().getSequenceAt(lastrow);
+ }
+
+ if (seq == null)
+ {
+ System.out.println(lastrow + " null");
+ continue;
+ }
+
+ for (col = 0; col < width; col++)
+ {
+ if ((int) (col * sampleCol) == lastcol
+ && (int) (row * sampleRow) == lastrow)
+ {
+ miniMe.setRGB(col, row, color);
+ continue;
+ }
+
+ lastcol = (int) (col * sampleCol);
+
+ if (seq.getLength() > lastcol)
+ {
+ color = sr.getResidueBoxColour(seq, lastcol).getRGB();
+
+ if (av.isShowSequenceFeatures())
+ {
+ color = fr.findFeatureColour(color, seq, lastcol);
+ }
+ }
+ else
+ {
+ color = -1; // White
+ }
+
+ if (hiddenRow
+ || (hasHiddenCols && !av.getColumnSelection().isVisible(
+ lastcol)))
+ {
+ color = new Color(color).darker().darker().getRGB();
+ }
+
+ miniMe.setRGB(col, row, color);
+
+ }
+ }
+
+ if (av.getAlignmentConservationAnnotation() != null)
+ {
+ renderer.updateFromAlignViewport(av);
+ for (col = 0; col < width; col++)
+ {
+ lastcol = (int) (col * sampleCol);
+ {
+ mg.translate(col, sequencesHeight);
+ renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
+ av.getAlignmentConservationAnnotation().annotations,
+ (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();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void setBoxPosition()
+ {
+ int fullsizeWidth = av.getAlignment().getWidth() * av.getCharWidth();
+ int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment()
+ .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.getAlignment().getHiddenSequences()
+ .adjustForHiddenSeqs(startSeq);
+
+ endSeq = av.getAlignment().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();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ */
+ @Override
+ public void paintComponent(Graphics g)
+ {
+ if (resizing)
+ {
+ g.setColor(Color.white);
+ g.fillRect(0, 0, getWidth(), getHeight());
+ }
+ else if (miniMe != null)
+ {
+ g.drawImage(miniMe, 0, 0, this);
+ }
+
+ g.setColor(Color.red);
+ g.drawRect(boxX, boxY, boxWidth, boxHeight);
+ g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
+
+ }
+}
git://source.jalview.org / jalview.git / blobdiff