-/*\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
-\r
-import javax.swing.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class OverviewPanel 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 = 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 = ap.av;\r
- this.ap = ap;\r
- setLayout(null);\r
-\r
- sr = new SequenceRenderer(av);\r
- sr.renderGaps( false );\r
- fr = new FeatureRenderer(av);\r
- fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;\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
- if(av.conservation==null)\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
- }\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
- if(!av.wrapAlignment)\r
- doMouseDragged(evt);\r
- }\r
- });\r
-\r
- addMouseListener(new MouseAdapter()\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
- });\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
- 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 ( (getWidth() > 0) && (getHeight() > 0))\r
- {\r
- width = getWidth();\r
- sequencesHeight = getHeight() - graphHeight;\r
- }\r
-\r
- setPreferredSize(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
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void run()\r
- {\r
- miniMe = null;\r
-\r
- int alwidth = av.alignment.getWidth();\r
- int alheight = av.alignment.getHeight();\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
-\r
- Graphics mg = miniMe.getGraphics();\r
- mg.setColor(Color.orange);\r
- mg.fillRect(0,0,width, miniMe.getHeight());\r
-\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
- miniMe.setRGB(col,row,color.getRGB());\r
- continue;\r
- }\r
-\r
- lastrow = (int)(row*sampleRow);\r
- lastcol = (int)(col*sampleCol);\r
-\r
- if(av.alignment.getSequenceAt(lastrow).getLength()>lastcol)\r
- {\r
- color = sr.getResidueBoxColour(\r
- av.alignment.getSequenceAt(lastrow), lastcol);\r
-\r
- if(av.showSequenceFeatures)\r
- color = fr.findFeatureColour(color, av.alignment.getSequenceAt(lastrow),\r
- lastcol);\r
-\r
- }\r
-\r
- miniMe.setRGB(col,row,color.getRGB());\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
- /**\r
- * DOCUMENT ME!\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) * av.getCharWidth() * scalew);\r
- boxHeight = (int) (av.getEndSeq() * av.getCharHeight() * scaleh) -\r
- boxY;\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 && !resizing)\r
- {\r
- g.drawImage(miniMe, 0, 0, this);\r
- }\r
- else\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, getWidth(), getHeight());\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
-\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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 jalview.viewmodel.OverviewDimensions;
+
+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;
+
+/**
+ * Panel displaying an overview of the full alignment, with an interactive box
+ * representing the viewport onto the alignment.
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class OverviewPanel extends JPanel implements Runnable
+{
+ private static final Color TRANS_GREY = new Color(100, 100, 100, 25);
+
+ private final AnnotationRenderer renderer = new AnnotationRenderer();
+
+ private OverviewDimensions od;
+
+ private BufferedImage miniMe;
+
+ private BufferedImage lastMiniMe = null;
+
+ private AlignViewport av;
+
+ private AlignmentPanel ap;
+
+ //
+ private boolean resizing = false;
+
+ // This is set true if the user resizes whilst
+ // the overview is being calculated
+ private boolean resizeAgain = false;
+
+ // Can set different properties in this seqCanvas than
+ // main visible SeqCanvas
+ private SequenceRenderer sr;
+
+ private jalview.renderer.seqfeatures.FeatureRenderer fr;
+
+ /**
+ * Creates a new OverviewPanel object.
+ *
+ * @param alPanel
+ * The alignment panel which is shown in the overview panel
+ */
+ public OverviewPanel(AlignmentPanel alPanel)
+ {
+ this.av = alPanel.av;
+ this.ap = alPanel;
+ setLayout(null);
+
+ sr = new SequenceRenderer(av);
+ sr.renderGaps = false;
+ sr.forOverview = true;
+ fr = new FeatureRenderer(alPanel);
+
+ od = new OverviewDimensions(av);
+
+ addComponentListener(new ComponentAdapter()
+ {
+ @Override
+ public void componentResized(ComponentEvent evt)
+ {
+ if ((getWidth() != od.getWidth())
+ || (getHeight() != (od.getHeight())))
+ {
+ 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.
+ od.setBoxPositionByMouse(evt.getX(), evt.getY());
+ ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
+ }
+ }
+ });
+
+ addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ if (!av.getWrapAlignment())
+ {
+ od.setBoxPositionByMouse(evt.getX(), evt.getY());
+ ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
+ }
+ }
+ });
+
+ updateOverviewImage();
+ }
+
+ /**
+ * Updates the overview image when the related alignment panel is updated
+ */
+ public void updateOverviewImage()
+ {
+ if (resizing)
+ {
+ resizeAgain = true;
+ return;
+ }
+
+ resizing = true;
+
+ if ((getWidth() > 0) && (getHeight() > 0))
+ {
+ od.setWidth(getWidth()); // width = getWidth();
+ od.setHeight(getHeight()); // sequencesHeight = getHeight() - graphHeight;
+ }
+
+ setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
+
+ Thread thread = new Thread(this);
+ thread.start();
+ repaint();
+ }
+
+ @Override
+ public void run()
+ {
+ miniMe = null;
+
+ if (av.isShowSequenceFeatures())
+ {
+ fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer());
+ }
+
+ // why do we need to set preferred size again? was set in
+ // updateOverviewImage
+ setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
+
+ miniMe = new BufferedImage(od.getWidth(), od.getHeight(),
+ BufferedImage.TYPE_INT_RGB);
+
+ Graphics mg = miniMe.getGraphics();
+ mg.setColor(Color.orange);
+ mg.fillRect(0, 0, od.getWidth(), miniMe.getHeight());
+
+ // calculate scale based on current alignment width and height
+ od.updateScales();
+
+ // calculate sampleCol and sampleRow
+ // alignment width is max number of residues/bases
+ // alignment height is number of sequences
+ int alwidth = av.getAlignment().getWidth();
+ int alheight = av.getAlignment().getHeight()
+ + av.getAlignment().getHiddenSequences().getSize();
+
+ // sampleCol or sampleRow is the width/height allocated to each residue
+ // in particular, sometimes we may need more than one row/col of the
+ // BufferedImage allocated
+ // sampleCol is how much of a residue to assign to each pixel
+ // sampleRow is how many sequences to assign to each pixel
+ float sampleCol = alwidth / (float) od.getWidth();
+ float sampleRow = alheight / (float) od.getSequencesHeight();
+
+ buildImage(sampleRow, sampleCol);
+
+ if (av.getAlignmentConservationAnnotation() != null)
+ {
+ renderer.updateFromAlignViewport(av);
+ for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
+ {
+ mg.translate(col, od.getSequencesHeight());
+ renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
+ av.getAlignmentConservationAnnotation().annotations,
+ (int) (sampleCol) + 1, od.getGraphHeight(),
+ (int) (col * sampleCol), (int) (col * sampleCol) + 1);
+ mg.translate(-col, -od.getSequencesHeight());
+
+ }
+ }
+ System.gc();
+
+ resizing = false;
+
+ if (resizeAgain)
+ {
+ resizeAgain = false;
+ updateOverviewImage();
+ }
+ else
+ {
+ lastMiniMe = miniMe;
+ }
+
+ setBoxPosition();
+ }
+
+ private void buildImage(float sampleRow, float sampleCol)
+ {
+ int lastcol = -1;
+ int lastrow = -1;
+ int color = Color.white.getRGB();
+
+ jalview.datamodel.SequenceI seq = null;
+ final boolean hasHiddenRows = av.hasHiddenRows();
+ final boolean hasHiddenCols = av.hasHiddenColumns();
+ boolean hiddenRow = false;
+ // get hidden row and hidden column map once at beginning.
+ // clone featureRenderer settings to avoid race conditions... if state is
+ // updated just need to refresh again
+ for (int row = 0; row < od.getSequencesHeight() && !resizeAgain; row++)
+ {
+ boolean doCopy = true;
+ int currentrow = (int) (row * sampleRow);
+ if (currentrow != lastrow)
+ {
+ doCopy = false;
+
+ lastrow = currentrow;
+
+ hiddenRow = false;
+ // should be method(s) in Alignment
+ 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);
+ }
+ // end of Alignment method(s)
+ }
+
+ if (seq == null)
+ {
+ System.out.println(lastrow + " null");
+ continue;
+ }
+
+ for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
+ {
+ if (doCopy)
+ {
+ color = miniMe.getRGB(col, row - 1);
+ }
+ else if ((int) (col * sampleCol) != lastcol
+ || (int) (row * sampleRow) != lastrow)
+ {
+ lastcol = (int) (col * sampleCol);
+ color = getColumnColourFromSequence(seq, hiddenRow, hasHiddenCols,
+ lastcol);
+ }
+ // else if ((int) (col * sampleCol) == lastcol && (int) (row *
+ // sampleRow) == lastrow))
+ // we just use the color we already have , so don't need to set it
+
+ miniMe.setRGB(col, row, color);
+ }
+ }
+ }
+
+ /*
+ * Find the colour of a sequence at a specified column position
+ */
+ private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq,
+ boolean hiddenRow, boolean hasHiddenCols, int lastcol)
+ {
+ int color;
+
+ if (seq.getLength() > lastcol)
+ {
+ color = sr.getResidueBoxColour(seq, lastcol).getRGB();
+
+ if (av.isShowSequenceFeatures())
+ {
+ color = fr.findFeatureColour(color, seq, lastcol);
+ }
+ }
+ else
+ {
+ color = Color.white.getRGB(); // White
+ }
+
+ if (hiddenRow
+ || (hasHiddenCols && !av.getColumnSelection()
+ .isVisible(lastcol)))
+ {
+ color = new Color(color).darker().darker().getRGB();
+ }
+
+ return color;
+ }
+
+ /**
+ * Update the overview panel box when the associated alignment panel is
+ * changed
+ *
+ */
+ public void setBoxPosition()
+ {
+ od.setBoxPosition();
+ repaint();
+ }
+
+
+ @Override
+ public void paintComponent(Graphics g)
+ {
+ if (resizing || resizeAgain)
+ {
+ if (lastMiniMe == null)
+ {
+ g.setColor(Color.white);
+ g.fillRect(0, 0, getWidth(), getHeight());
+ }
+ else
+ {
+ g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
+ }
+ g.setColor(TRANS_GREY);
+ g.fillRect(0, 0, getWidth(), getHeight());
+ }
+ else if (lastMiniMe != null)
+ {
+ g.drawImage(lastMiniMe, 0, 0, this);
+ if (lastMiniMe != miniMe)
+ {
+ g.setColor(TRANS_GREY);
+ g.fillRect(0, 0, getWidth(), getHeight());
+ }
+ }
+ // TODO: render selected regions
+ g.setColor(Color.red);
+ od.drawBox(g);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff