-/*\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.event.*;\r
-import java.awt.*;\r
-\r
-public class OverviewPanel extends Panel implements Runnable\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=30;\r
- int boxX=-1, boxY=-1, boxWidth=-1, boxHeight=-1;\r
-\r
- boolean resizing = false;\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
- // scale the initial size of overviewpanel to shape of alignment\r
- float initialScale = (float)av.alignment.getWidth()/(float)av.alignment.getHeight();\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
- if(width<120)\r
- width = 120;\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 || getSize().height!=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
- addMouseListener(new MouseAdapter()\r
- {\r
- public void mousePressed(MouseEvent evt)\r
- { doMousePressed(evt);}\r
- public void mouseReleased(MouseEvent evt)\r
- { doMouseReleased(evt);}\r
- });\r
-\r
- updateOverviewImage();\r
-\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
- if(!resizing)\r
- ap.setScrollValues( (int)(boxX/scalew/av.getCharWidth()),\r
- (int)(boxY/scaleh/av.getCharHeight()) );\r
- }\r
-\r
- public void doMouseDragged(MouseEvent evt)\r
- {\r
- boxX = evt.getX();\r
- boxY = evt.getY();\r
- checkValid();\r
- if(!resizing)\r
- ap.setScrollValues( (int)(boxX/scalew/av.getCharWidth()),\r
- (int)(boxY/scaleh/av.getCharHeight()) );\r
- repaint();\r
- ap.repaint();\r
- }\r
-\r
- void checkValid()\r
- {\r
- if (boxY < 0)\r
- boxY = 0;\r
-\r
- if (boxY > sequencesHeight - boxHeight)\r
- boxY = sequencesHeight - boxHeight+1;\r
-\r
- if (boxX < 0)\r
- boxX = 0;\r
-\r
- if (boxX > width - boxWidth)\r
- boxX = width - boxWidth;\r
- }\r
-\r
- public void updateOverviewImage()\r
- {\r
- if(resizing)\r
- {\r
- return;\r
- }\r
-\r
- resizing = true;\r
- Thread thread = new Thread(this);\r
- thread.start();\r
- repaint();\r
- }\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
- Image consensus = nullFrame.createImage(fullsizeWidth, 60);\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
-\r
- boolean oldRenderGaps = av.renderGaps;\r
- try{\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
-\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
- Image block;\r
- int blockx=0, blocky=0, blockw=0, blockh=0, eRes=0, eSeq=0;\r
-\r
- av.setRenderGaps(false);\r
- for(int sRes=0, chunkx=0; sRes<alwidth; sRes+=maxSize, chunkx++)\r
- {\r
- eSeq = 0;\r
- eRes+=maxSize;\r
- if(eRes>alwidth)\r
- eRes = alwidth;\r
-\r
- for(int sSeq=0, chunky=0; sSeq<alheight; sSeq+=maxSize, chunky++)\r
- {\r
- eSeq+=maxSize;\r
- if(eSeq>alheight)\r
- eSeq = alheight;\r
-\r
- blocky = 0;\r
- blockx = (int)((float)sRes/(float)alwidth * width);\r
-\r
- block = nullFrame.createImage((eRes-sRes)*av.charWidth, (eSeq-sSeq)*av.charHeight);\r
- g = block.getGraphics();\r
-\r
- ap.seqPanel.seqCanvas.drawPanel(g, sRes, eRes, sSeq, eSeq, sRes, sSeq, 0);\r
-\r
- blockh = (int)( (float)(eSeq-sSeq)/(float)alheight * sequencesHeight )+1 ;\r
- blockw = (int)( (float)(eRes-sRes)/(float)alwidth * width )+1;\r
-\r
- blocky += (int) ((float)sSeq/(float)alheight* sequencesHeight);\r
-\r
- mg.drawImage(block, blockx,\r
- blocky ,\r
- blockx + blockw,\r
- blocky + blockh,\r
-\r
- 0, 0, block.getWidth(null),block.getHeight(null), this);\r
-\r
- block = null;\r
- }\r
-\r
- }\r
-\r
- }catch(OutOfMemoryError error)\r
- { System.err.println("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)* 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(resizing)\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, getSize().width, getSize().height);\r
- g.setColor(Color.black);\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
- g.drawImage(miniMe, 0,0,this);\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
-}\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.appletgui;
+
+import jalview.datamodel.AlignmentI;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.Panel;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+
+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);
+
+ // scale the initial size of overviewpanel to shape of alignment
+ float initialScale = (float) av.getAlignment().getWidth()
+ / (float) av.getAlignment().getHeight();
+
+ if (av.getSequenceConsensusHash() == 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;
+ }
+ }
+
+ setSize(new Dimension(width, sequencesHeight + graphHeight));
+ addComponentListener(new ComponentAdapter()
+ {
+
+ @Override
+ public void componentResized(ComponentEvent evt)
+ {
+ if (getSize().width != width
+ || getSize().height != sequencesHeight + graphHeight)
+ {
+ updateOverviewImage();
+ }
+ }
+ });
+
+ addMouseMotionListener(this);
+
+ addMouseListener(this);
+
+ updateOverviewImage();
+
+ }
+
+ @Override
+ public void mouseEntered(MouseEvent evt)
+ {
+ }
+
+ @Override
+ public void mouseExited(MouseEvent evt)
+ {
+ }
+
+ @Override
+ public void mouseClicked(MouseEvent evt)
+ {
+ }
+
+ @Override
+ public void mouseMoved(MouseEvent evt)
+ {
+ }
+
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ boxX = evt.getX();
+ boxY = evt.getY();
+ checkValid();
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ boxX = evt.getX();
+ boxY = evt.getY();
+ checkValid();
+ }
+
+ @Override
+ 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.getAlignment().getHiddenSequences()
+ .findIndexWithoutHiddenSeqs(row);
+ }
+
+ ap.setScrollValues(col, row);
+ ap.paintAlignment(false);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void updateOverviewImage()
+ {
+ if (resizing)
+ {
+ resizeAgain = true;
+ return;
+ }
+
+ if (av.isShowSequenceFeatures())
+ {
+ fr.transferSettings(ap.seqPanel.seqCanvas.fr);
+ }
+
+ 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;
+
+ @Override
+ public void run()
+ {
+ miniMe = null;
+ int alwidth = av.getAlignment().getWidth();
+ int alheight = av.getAlignment().getHeight();
+
+ if (av.isShowSequenceFeatures())
+ {
+ 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;
+ final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
+ .hasHiddenColumns();
+ boolean hiddenRow = false;
+ AlignmentI alignment = av.getAlignment();
+ for (row = 0; row <= sequencesHeight; row++)
+ {
+ if ((int) (row * sampleRow) == lastrow)
+ {
+ sameRow++;
+ continue;
+ }
+
+ hiddenRow = false;
+ if (hasHiddenRows)
+ {
+ seq = alignment.getHiddenSequences().getHiddenSequence(lastrow);
+ if (seq == null)
+ {
+ int index = alignment.getHiddenSequences()
+ .findIndexWithoutHiddenSeqs(lastrow);
+
+ seq = alignment.getSequenceAt(index);
+ }
+ else
+ {
+ hiddenRow = true;
+ }
+ }
+ else
+ {
+ seq = 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.isShowSequenceFeatures())
+ {
+ color = fr.findFeatureColour(color, seq, lastcol);
+ }
+ }
+ else
+ {
+ color = Color.white; // White
+ }
+
+ if (hiddenRow
+ || (hasHiddenCols && !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.getAlignmentConservationAnnotation() != null)
+ {
+ for (col = 0; col < width; col++)
+ {
+ lastcol = (int) (col * sampleCol);
+ {
+ mg.translate(col, sequencesHeight);
+ ap.annotationPanel.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();
+ }
+ }
+
+ 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();
+ }
+
+ @Override
+ public void update(Graphics g)
+ {
+ paint(g);
+ }
+
+ @Override
+ 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