-package jalview.gui;\r
-\r
-import java.awt.*;\r
-import javax.swing.*;\r
-import java.awt.event.*;\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-import jalview.analysis.*;\r
-\r
-\r
-public class SeqCanvas extends JPanel\r
-{\r
- Image img;\r
- Graphics gg;\r
- int imgWidth;\r
- int imgHeight;\r
-\r
- AlignViewport av;\r
-\r
- public boolean paintFlag = false;\r
-\r
- boolean showScores = false;\r
- boolean displaySearch = false;\r
- int [] searchResults = null;\r
-\r
- int chunkHeight;\r
- int chunkWidth;\r
-\r
-\r
- public SeqCanvas(AlignViewport av)\r
- {\r
- this.av = av;\r
- setLayout(new BorderLayout());\r
- PaintRefresher.Register(this);\r
-\r
- }\r
-\r
- public void drawScale(int startx, int endx,int charWidth, int charHeight,int ypos) {\r
- int scalestartx = startx - startx%10 + 10;\r
-\r
- gg.setColor(Color.black);\r
-\r
- for (int i=scalestartx;i < endx;i+= 10) {\r
- String string = String.valueOf(i);\r
- gg.drawString(string,(int)((i-startx-1)*charWidth),ypos+15 - charHeight*(2));\r
- }\r
- }\r
-\r
-\r
-/**\r
- * Definitions of startx and endx (hopefully):\r
- * SMJS This is what I'm working towards!\r
- * startx is the first residue (starting at 0) to display.\r
- * endx is the last residue to display (starting at 0).\r
- * starty is the first sequence to display (starting at 0).\r
- * endy is the last sequence to display (starting at 0).\r
- * NOTE 1: The av limits are set in setFont in this class and\r
- * in the adjustment listener in SeqPanel when the scrollbars move.\r
- */\r
-\r
- public void paintComponent(Graphics g) {\r
-\r
- AlignmentI da = av.getAlignment();\r
-\r
- if (img == null ||\r
- imgWidth != getWidth() ||\r
- imgHeight != getHeight()\r
- || paintFlag)\r
- {\r
-\r
- imgWidth = getWidth();\r
- imgHeight = getHeight();\r
-\r
- img = createImage(imgWidth,imgHeight);\r
- gg = img.getGraphics();\r
-\r
- gg.setFont(av.getFont());\r
-\r
- paintFlag = false;\r
- }\r
-\r
- chunkWidth = getWidth()/av.charWidth;\r
- chunkHeight = (da.getHeight() + 2)*av.charHeight;\r
-\r
- av.setChunkHeight(chunkHeight);\r
- av.setChunkWidth(chunkWidth);\r
-\r
-\r
-\r
- fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight);\r
-\r
- /* if (av.getWrapAlignment()) {\r
- int offy = av.getStartSeq();\r
- startx = (int)(offy/chunkWidth)*chunkWidth;\r
- endx = startx + chunkWidth;\r
- starty = offy%chunkHeight;\r
- endy = starty + da.getHeight();\r
-\r
- int ypos = 0;\r
- int rowstart = starty;\r
-\r
- if (starty == 0) {\r
- ypos = 2*charHeight;\r
- } else if (starty == 1) {\r
- starty = 0;\r
- ypos = charHeight;\r
- }\r
-\r
- if (endy > da.getHeight()) {\r
- endy = da.getHeight();\r
- }\r
-\r
- if (endx > da.getWidth()) {\r
- endx = da.getWidth();\r
- }\r
-\r
- if (rowstart < 2) {\r
- drawScale(startx,endx,charWidth,charHeight,ypos);\r
- }\r
-\r
- drawPanel(gg,startx,endx,starty,endy,startx,starty,ypos);\r
-\r
- if (rowstart == 0) {\r
- ypos = ypos + chunkHeight;\r
- } else if (rowstart == 1) {\r
- ypos = ypos + chunkHeight;\r
- } else {\r
- ypos = ypos + chunkHeight - rowstart*charHeight;\r
- }\r
-\r
- startx += chunkWidth;\r
- endx = startx + chunkWidth;\r
- starty = 0;\r
-\r
- if (endx > da.getWidth()) {\r
- endx = da.getWidth();\r
- }\r
- // Draw the rest of the panels\r
-\r
- while (ypos <= getHeight()) {\r
- drawScale(startx,endx,charWidth,charHeight,ypos);\r
- drawPanel(gg,startx,endx,0,da.getHeight(),startx,starty,ypos);\r
-\r
- ypos += chunkHeight;\r
- startx += chunkWidth;\r
- endx = startx + chunkWidth;\r
-\r
- if (endy > da.getHeight()) {\r
- endy = da.getHeight();\r
- }\r
-\r
- if (endx > da.getWidth()) {\r
- endx = da.getWidth();\r
- }\r
-\r
- }\r
- }\r
- else*/\r
- {\r
- drawPanel(gg,av.startRes,av.endRes,av.startSeq,av.endSeq,av.startRes,av.startSeq,0);\r
- }\r
-\r
-\r
- /* if ((oldendy -oldstarty) > (getWidth() / av.getCharWidth())) {\r
- System.out.println("LIMITS ERROR LIMITS ERROR");\r
- System.out.println("Corrds " + (oldendy-oldstarty) + " " + (getWidth()/av.getCharWidth()) + " " + getWidth() + " " + av.getCharWidth());\r
- }*/\r
-\r
- g.drawImage(img,0,0,this);\r
-\r
- }\r
-\r
-\r
-\r
-\r
- public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {\r
-\r
-\r
- g.setFont(av.getFont());\r
- int charWidth = av.getCharWidth();\r
- int charHeight = av.getCharHeight();\r
- RendererI sr = av.getRenderer();\r
-\r
- /*Vector pid = av.getConsensus(false);\r
- Vector tmpseq = new Vector();\r
- for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
- if (!av.getSelection().contains(av.getAlignment().getSequenceAt(i)))\r
- tmpseq.addElement(av.getAlignment().getSequenceAt(i));\r
-\r
- if (sr instanceof SequenceRenderer)\r
- pid = AAFrequency.calculate(tmpseq,x1,x2);\r
-\r
- else if (sr instanceof GraphRenderer)\r
- pid = AAFrequency.calculatePID(av.getAlignment().getSequenceAt(0),\r
- av.getAlignment().getSequences(),\r
- av.getPIDWindow(),x1,x2);\r
-\r
-*/\r
-\r
- /* if (y2 > starty && y1 < av.getEndSeq())\r
- {\r
- fillBackground(g,\r
- Color.red,\r
- (x1-startx)*charWidth,\r
- offset + AlignmentUtil.getPixelHeight(starty,y1,av.getCharHeight()),\r
- (x2-x1+1)*charWidth,\r
- offset + AlignmentUtil.getPixelHeight(y1,y2,av.getCharHeight()));\r
- }*/\r
-\r
- SequenceI nextSeq;\r
- SequenceGroup group=null;\r
- boolean inGroup=false; // are we in a defined group?\r
- boolean inRB=false; //Are we in a rubberband group?\r
- int sx=-1, sy=-1, ex=-1, ey=-1;\r
- int oldStartX=0,oldEndX=0,oldY=0;\r
- int oldRStartX=0,oldREndX=0,oldRY=0;\r
- for (int i = y1 ; i < y2 ;i++)\r
- {\r
- nextSeq = av.getAlignment().getSequenceAt(i);\r
-\r
- group = av.alignment.findGroup( nextSeq );\r
-\r
- sr.drawSequence(g, nextSeq, group,x1,x2,\r
- (x1 - startx) * charWidth,\r
- offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()),\r
- charWidth,charHeight,null, i);\r
-\r
-\r
- if( group!=null )\r
- {\r
-\r
- g.setColor(Color.lightGray);\r
-\r
- sx = (group.getStartRes()-startx)*charWidth;\r
- sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight());\r
- ex = (group.getEndRes()+1-startx)*charWidth;\r
- ey = offset + AlignmentUtil.getPixelHeight(starty, i+1, av.getCharHeight());\r
-\r
-\r
- if (!inGroup)\r
- {\r
- g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box\r
- inGroup=true;\r
- }\r
-\r
- g.drawLine(sx, sy, sx, ey ); // vertical line, left hand side\r
- g.drawLine( ex,sy,ex,ey); // vertical line, right hand side\r
- if (i == y2 - 1)// last line of alignment, seal the box\r
- g.drawLine(sx, ey, ex, ey); // Horizontal, bottom of old box\r
-\r
- oldStartX = sx;\r
- oldEndX = ex;\r
- oldY = ey;\r
-\r
- }\r
- else if(inGroup)\r
- {\r
- g.setColor(Color.lightGray);\r
- g.drawLine(oldStartX, oldY, oldEndX, oldY); // Horizontal, bottom of old box\r
- }\r
- else\r
- inGroup = false;\r
-\r
- group = av.getRubberbandGroup();\r
- if( group != null && group.sequences.contains(nextSeq) )\r
- {\r
- g.setColor(Color.RED.brighter());\r
- sx = (group.getStartRes() - startx) * charWidth;\r
- sy = offset +\r
- AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight());\r
- ex = (group.getEndRes() + 1 - startx) * charWidth;\r
- ey = offset +\r
- AlignmentUtil.getPixelHeight(starty, i + 1, av.getCharHeight());\r
-\r
- if (!inRB)\r
- {\r
-\r
- g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box\r
- inRB = true;\r
- }\r
-\r
- g.drawLine(sx, sy, sx, ey); // vertical line, left hand side\r
- g.drawLine(ex, sy, ex, ey); // vertical line, right hand side\r
- if (i == y2 - 1) // last line of alignment, seal the box\r
- g.drawLine(sx, ey, ex, ey); // Horizontal, bottom of old box\r
-\r
- oldRStartX = sx;\r
- oldREndX = ex;\r
- oldRY = ey;\r
- }\r
- else if(inRB)\r
- {\r
- g.setColor(Color.RED.brighter());\r
- g.drawLine(oldRStartX, oldRY, oldREndX, oldRY); // Horizontal, bottom of old box\r
- inRB = false;\r
- }\r
- else\r
- inRB = false;\r
-\r
- }\r
-\r
- /// Highlight search Results once all sequences have been drawn\r
- if(displaySearch)\r
- {\r
- for(int r=0; r<searchResults.length; r+=3)\r
- {\r
- int searchSeq = searchResults[r];\r
- int searchStart = searchResults[r+1];\r
- int searchEnd = searchResults[r+2];\r
-\r
- if (searchSeq >= y1 && searchSeq <= y2)\r
- {\r
- SequenceRenderer ssr = (SequenceRenderer) sr;\r
- ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq),\r
- searchStart,\r
- searchEnd,\r
- (searchStart - startx) * charWidth,\r
- offset +\r
- AlignmentUtil.getPixelHeight(starty, searchSeq,\r
- charHeight),\r
- charWidth,\r
- charHeight);\r
- }\r
- }\r
- }\r
-\r
- }\r
-\r
- public void fillBackground(Graphics g,Color c, int x1,int y1,int width,int height) {\r
- g.setColor(c);\r
- g.fillRect(x1,y1,width,height);\r
- }\r
-\r
- public int getChunkWidth() {\r
- return chunkWidth;\r
- }\r
-\r
- public void highlightSearchResults(int [] results)\r
- {\r
- // results are in the order sequence, startRes, endRes\r
- if(results==null)\r
- displaySearch = false;\r
- else\r
- displaySearch = true;\r
-\r
- searchResults = results;\r
-\r
- paintFlag = true;\r
- repaint();\r
- }\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.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.ScaleRenderer;
+import jalview.renderer.ScaleRenderer.ScaleMark;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
+import java.awt.AlphaComposite;
+import java.awt.BasicStroke;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+import java.awt.Shape;
+import java.awt.image.BufferedImage;
+import java.beans.PropertyChangeEvent;
+import java.util.List;
+
+import javax.swing.JComponent;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SeqCanvas extends JComponent implements ViewportListenerI
+{
+ final FeatureRenderer fr;
+
+ final SequenceRenderer seqRdr;
+
+ BufferedImage img;
+
+ Graphics2D gg;
+
+ AlignViewport av;
+
+ boolean fastPaint = false;
+
+ int LABEL_WEST;
+
+ int LABEL_EAST;
+
+ int cursorX = 0;
+
+ int cursorY = 0;
+
+ int charHeight = 0;
+
+ int charWidth = 0;
+
+ boolean fastpainting = false;
+
+ AnnotationPanel annotations;
+
+ /**
+ * Creates a new SeqCanvas object.
+ *
+ * @param av
+ * DOCUMENT ME!
+ */
+ public SeqCanvas(AlignmentPanel ap)
+ {
+ this.av = ap.av;
+ updateViewport();
+ fr = new FeatureRenderer(ap);
+ seqRdr = new SequenceRenderer(av);
+ setLayout(new BorderLayout());
+ PaintRefresher.Register(this, av.getSequenceSetId());
+ setBackground(Color.white);
+
+ av.getRanges().addPropertyChangeListener(this);
+ }
+
+ public SequenceRenderer getSequenceRenderer()
+ {
+ return seqRdr;
+ }
+
+ public FeatureRenderer getFeatureRenderer()
+ {
+ return fr;
+ }
+
+ private void updateViewport()
+ {
+ charHeight = av.getCharHeight();
+ charWidth = av.getCharWidth();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param startx
+ * DOCUMENT ME!
+ * @param endx
+ * DOCUMENT ME!
+ * @param ypos
+ * DOCUMENT ME!
+ */
+ private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
+ {
+ updateViewport();
+ for (ScaleMark mark : new ScaleRenderer().calculateMarks(av, startx,
+ endx))
+ {
+ int mpos = mark.column; // (i - startx - 1)
+ if (mpos < 0)
+ {
+ continue;
+ }
+ String mstring = mark.text;
+
+ if (mark.major)
+ {
+ if (mstring != null)
+ {
+ g.drawString(mstring, mpos * charWidth, ypos - (charHeight / 2));
+ }
+ g.drawLine((mpos * charWidth) + (charWidth / 2),
+ (ypos + 2) - (charHeight / 2),
+ (mpos * charWidth) + (charWidth / 2), ypos - 2);
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param startx
+ * DOCUMENT ME!
+ * @param endx
+ * DOCUMENT ME!
+ * @param ypos
+ * DOCUMENT ME!
+ */
+ void drawWestScale(Graphics g, int startx, int endx, int ypos)
+ {
+ FontMetrics fm = getFontMetrics(av.getFont());
+ ypos += charHeight;
+
+ if (av.hasHiddenColumns())
+ {
+ startx = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(startx);
+ endx = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(endx);
+ }
+
+ int maxwidth = av.getAlignment().getWidth();
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth) - 1;
+ }
+
+ // WEST SCALE
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)
+ {
+ SequenceI seq = av.getAlignment().getSequenceAt(i);
+ int index = startx;
+ int value = -1;
+
+ while (index < endx)
+ {
+ if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+ {
+ index++;
+
+ continue;
+ }
+
+ value = av.getAlignment().getSequenceAt(i).findPosition(index);
+
+ break;
+ }
+
+ if (value != -1)
+ {
+ int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
+ - charWidth / 2;
+ g.drawString(value + "", x,
+ (ypos + (i * charHeight)) - (charHeight / 5));
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param startx
+ * DOCUMENT ME!
+ * @param endx
+ * DOCUMENT ME!
+ * @param ypos
+ * DOCUMENT ME!
+ */
+ void drawEastScale(Graphics g, int startx, int endx, int ypos)
+ {
+ ypos += charHeight;
+
+ if (av.hasHiddenColumns())
+ {
+ endx = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(endx);
+ }
+
+ SequenceI seq;
+ // EAST SCALE
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)
+ {
+ seq = av.getAlignment().getSequenceAt(i);
+ int index = endx;
+ int value = -1;
+
+ while (index > startx)
+ {
+ if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+ {
+ index--;
+
+ continue;
+ }
+
+ value = seq.findPosition(index);
+
+ break;
+ }
+
+ if (value != -1)
+ {
+ g.drawString(String.valueOf(value), 0,
+ (ypos + (i * charHeight)) - (charHeight / 5));
+ }
+ }
+ }
+
+
+ /**
+ * need to make this thread safe move alignment rendering in response to
+ * slider adjustment
+ *
+ * @param horizontal
+ * shift along
+ * @param vertical
+ * shift up or down in repaint
+ */
+ public void fastPaint(int horizontal, int vertical)
+ {
+ if (fastpainting || gg == null)
+ {
+ return;
+ }
+ fastpainting = true;
+ fastPaint = true;
+ updateViewport();
+
+ ViewportRanges ranges = av.getRanges();
+ int sr = ranges.getStartRes();
+ int er = ranges.getEndRes();
+ int ss = ranges.getStartSeq();
+ int es = ranges.getEndSeq();
+ int transX = 0;
+ int transY = 0;
+
+ gg.copyArea(horizontal * charWidth, vertical * charHeight,
+ img.getWidth(), img.getHeight(), -horizontal * charWidth,
+ -vertical * charHeight);
+
+ if (horizontal > 0) // scrollbar pulled right, image to the left
+ {
+ transX = (er - sr - horizontal) * charWidth;
+ sr = er - horizontal;
+ }
+ else if (horizontal < 0)
+ {
+ er = sr - horizontal;
+ }
+ else if (vertical > 0) // scroll down
+ {
+ ss = es - vertical;
+
+ if (ss < ranges.getStartSeq())
+ { // ie scrolling too fast, more than a page at a time
+ ss = ranges.getStartSeq();
+ }
+ else
+ {
+ transY = img.getHeight() - ((vertical + 1) * charHeight);
+ }
+ }
+ else if (vertical < 0)
+ {
+ es = ss - vertical;
+
+ if (es > ranges.getEndSeq())
+ {
+ es = ranges.getEndSeq();
+ }
+ }
+
+ gg.translate(transX, transY);
+ drawPanel(gg, sr, er, ss, es, 0);
+ gg.translate(-transX, -transY);
+
+ repaint();
+ fastpainting = false;
+ }
+
+ /**
+ * Definitions of startx and endx (hopefully): SMJS This is what I'm working
+ * towards! startx is the first residue (starting at 0) to display. endx is
+ * the last residue to display (starting at 0). starty is the first sequence
+ * to display (starting at 0). endy is the last sequence to display (starting
+ * at 0). NOTE 1: The av limits are set in setFont in this class and in the
+ * adjustment listener in SeqPanel when the scrollbars move.
+ */
+
+ // Set this to false to force a full panel paint
+ @Override
+ public void paintComponent(Graphics g)
+ {
+ super.paintComponent(g);
+
+ updateViewport();
+
+ ViewportRanges ranges = av.getRanges();
+
+ int width = getWidth();
+ int height = getHeight();
+
+ width -= (width % charWidth);
+ height -= (height % charHeight);
+
+ // selectImage is the selection group outline image
+ BufferedImage selectImage = drawSelectionGroup(
+ ranges.getStartRes(), ranges.getEndRes(),
+ ranges.getStartSeq(), ranges.getEndSeq());
+
+ if ((img != null) && (fastPaint
+ || (getVisibleRect().width != g.getClipBounds().width)
+ || (getVisibleRect().height != g.getClipBounds().height)))
+ {
+ BufferedImage lcimg = buildLocalImage(selectImage);
+ g.drawImage(lcimg, 0, 0, this);
+ fastPaint = false;
+ }
+ else if ((width > 0) && (height > 0))
+ {
+ // img is a cached version of the last view we drew, if any
+ // if we have no img or the size has changed, make a new one
+ if (img == null || width != img.getWidth()
+ || height != img.getHeight())
+ {
+ img = setupImage();
+ if (img == null)
+ {
+ return;
+ }
+ gg = (Graphics2D) img.getGraphics();
+ gg.setFont(av.getFont());
+ }
+
+ if (av.antiAlias)
+ {
+ gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ }
+
+ gg.setColor(Color.white);
+ gg.fillRect(0, 0, img.getWidth(), img.getHeight());
+
+ if (av.getWrapAlignment())
+ {
+ drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
+ }
+ else
+ {
+ drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
+ ranges.getStartSeq(), ranges.getEndSeq(), 0);
+ }
+
+ // lcimg is a local *copy* of img which we'll draw selectImage on top of
+ BufferedImage lcimg = buildLocalImage(selectImage);
+ g.drawImage(lcimg, 0, 0, this);
+ }
+ }
+
+ /**
+ * Draw an alignment panel for printing
+ *
+ * @param g1
+ * Graphics object to draw with
+ * @param startRes
+ * start residue of print area
+ * @param endRes
+ * end residue of print area
+ * @param startSeq
+ * start sequence of print area
+ * @param endSeq
+ * end sequence of print area
+ */
+ public void drawPanelForPrinting(Graphics g1, int startRes, int endRes,
+ int startSeq, int endSeq)
+ {
+ BufferedImage selectImage = drawSelectionGroup(startRes, endRes,
+ startSeq, endSeq);
+ drawPanel(g1, startRes, endRes, startSeq, endSeq, 0);
+ ((Graphics2D) g1).setComposite(
+ AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
+ g1.drawImage(selectImage, 0, 0, this);
+ }
+
+ /**
+ * Draw a wrapped alignment panel for printing
+ *
+ * @param g
+ * Graphics object to draw with
+ * @param canvasWidth
+ * width of drawing area
+ * @param canvasHeight
+ * height of drawing area
+ * @param startRes
+ * start residue of print area
+ */
+ public void drawWrappedPanelForPrinting(Graphics g, int canvasWidth,
+ int canvasHeight, int startRes)
+ {
+ SequenceGroup group = av.getSelectionGroup();
+
+ drawWrappedPanel(g, canvasWidth, canvasHeight, startRes);
+
+ if (group != null)
+ {
+ BufferedImage selectImage = null;
+ try
+ {
+ selectImage = new BufferedImage(canvasWidth, canvasHeight,
+ BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works
+ } catch (OutOfMemoryError er)
+ {
+ System.gc();
+ System.err.println("Print image OutOfMemory Error.\n" + er);
+ new OOMWarning("Creating wrapped alignment image for printing", er);
+ }
+ if (selectImage != null)
+ {
+ Graphics2D g2 = selectImage.createGraphics();
+ setupSelectionGroup(g2, selectImage);
+ drawWrappedSelection(g2, group, canvasWidth, canvasHeight,
+ startRes);
+
+ g2.setComposite(
+ AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
+ g.drawImage(selectImage, 0, 0, this);
+ g2.dispose();
+ }
+ }
+ }
+
+ /*
+ * Make a local image by combining the cached image img
+ * with any selection
+ */
+ private BufferedImage buildLocalImage(BufferedImage selectImage)
+ {
+ // clone the cached image
+ BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(),
+ img.getType());
+ Graphics2D g2d = lcimg.createGraphics();
+ g2d.drawImage(img, 0, 0, null);
+
+ // overlay selection group on lcimg
+ if (selectImage != null)
+ {
+ g2d.setComposite(
+ AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
+ g2d.drawImage(selectImage, 0, 0, this);
+ }
+ g2d.dispose();
+
+ return lcimg;
+ }
+
+ /*
+ * Set up a buffered image of the correct height and size for the sequence canvas
+ */
+ private BufferedImage setupImage()
+ {
+ BufferedImage lcimg = null;
+
+ int width = getWidth();
+ int height = getHeight();
+
+ width -= (width % charWidth);
+ height -= (height % charHeight);
+
+ if ((width < 1) || (height < 1))
+ {
+ return null;
+ }
+
+ try
+ {
+ lcimg = new BufferedImage(width, height,
+ BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works
+ } catch (OutOfMemoryError er)
+ {
+ System.gc();
+ System.err.println(
+ "Group image OutOfMemory Redraw Error.\n" + er);
+ new OOMWarning("Creating alignment image for display", er);
+
+ return null;
+ }
+
+ return lcimg;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cwidth
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getWrappedCanvasWidth(int cwidth)
+ {
+ FontMetrics fm = getFontMetrics(av.getFont());
+
+ LABEL_EAST = 0;
+ LABEL_WEST = 0;
+
+ if (av.getScaleRightWrapped())
+ {
+ LABEL_EAST = fm.stringWidth(getMask());
+ }
+
+ if (av.getScaleLeftWrapped())
+ {
+ LABEL_WEST = fm.stringWidth(getMask());
+ }
+
+ return (cwidth - LABEL_EAST - LABEL_WEST) / charWidth;
+ }
+
+ /**
+ * Generates a string of zeroes.
+ *
+ * @return String
+ */
+ String getMask()
+ {
+ String mask = "00";
+ int maxWidth = 0;
+ int tmp;
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)
+ {
+ tmp = av.getAlignment().getSequenceAt(i).getEnd();
+ if (tmp > maxWidth)
+ {
+ maxWidth = tmp;
+ }
+ }
+
+ for (int i = maxWidth; i > 0; i /= 10)
+ {
+ mask += "0";
+ }
+ return mask;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param canvasWidth
+ * DOCUMENT ME!
+ * @param canvasHeight
+ * DOCUMENT ME!
+ * @param startRes
+ * DOCUMENT ME!
+ */
+ private void drawWrappedPanel(Graphics g, int canvasWidth,
+ int canvasHeight, int startRes)
+ {
+ updateViewport();
+ AlignmentI al = av.getAlignment();
+
+ FontMetrics fm = getFontMetrics(av.getFont());
+
+ LABEL_EAST = 0;
+ LABEL_WEST = 0;
+
+ if (av.getScaleRightWrapped())
+ {
+ LABEL_EAST = fm.stringWidth(getMask());
+ }
+
+ if (av.getScaleLeftWrapped())
+ {
+ LABEL_WEST = fm.stringWidth(getMask());
+ }
+
+ int hgap = charHeight;
+ if (av.getScaleAboveWrapped())
+ {
+ hgap += charHeight;
+ }
+
+ int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / charWidth;
+ int cHeight = av.getAlignment().getHeight() * charHeight;
+
+ av.setWrappedWidth(cWidth);
+
+ av.getRanges().setViewportStartAndWidth(startRes, cWidth);
+
+ int endx;
+ int ypos = hgap;
+ int maxwidth = av.getAlignment().getWidth();
+
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth);
+ }
+
+ while ((ypos <= canvasHeight) && (startRes < maxwidth))
+ {
+ endx = startRes + cWidth - 1;
+
+ if (endx > maxwidth)
+ {
+ endx = maxwidth;
+ }
+
+ g.setFont(av.getFont());
+ g.setColor(Color.black);
+
+ if (av.getScaleLeftWrapped())
+ {
+ drawWestScale(g, startRes, endx, ypos);
+ }
+
+ if (av.getScaleRightWrapped())
+ {
+ g.translate(canvasWidth - LABEL_EAST, 0);
+ drawEastScale(g, startRes, endx, ypos);
+ g.translate(-(canvasWidth - LABEL_EAST), 0);
+ }
+
+ g.translate(LABEL_WEST, 0);
+
+ if (av.getScaleAboveWrapped())
+ {
+ drawNorthScale(g, startRes, endx, ypos);
+ }
+
+ if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
+ {
+ g.setColor(Color.blue);
+ int res;
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ List<Integer> positions = hidden.findHiddenRegionPositions();
+ for (int pos : positions)
+ {
+ res = pos - startRes;
+
+ if (res < 0 || res > endx - startRes)
+ {
+ continue;
+ }
+
+ gg.fillPolygon(
+ new int[]
+ { res * charWidth - charHeight / 4,
+ res * charWidth + charHeight / 4, res * charWidth },
+ new int[]
+ { ypos - (charHeight / 2), ypos - (charHeight / 2),
+ ypos - (charHeight / 2) + 8 },
+ 3);
+
+ }
+ }
+
+ // When printing we have an extra clipped region,
+ // the Printable page which we need to account for here
+ Shape clip = g.getClip();
+
+ if (clip == null)
+ {
+ g.setClip(0, 0, cWidth * charWidth, canvasHeight);
+ }
+ else
+ {
+ g.setClip(0, (int) clip.getBounds().getY(), cWidth * charWidth,
+ (int) clip.getBounds().getHeight());
+ }
+
+ drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos);
+
+ if (av.isShowAnnotation())
+ {
+ g.translate(0, cHeight + ypos + 3);
+ if (annotations == null)
+ {
+ annotations = new AnnotationPanel(av);
+ }
+
+ annotations.renderer.drawComponent(annotations, av, g, -1, startRes,
+ endx + 1);
+ g.translate(0, -cHeight - ypos - 3);
+ }
+ g.setClip(clip);
+ g.translate(-LABEL_WEST, 0);
+
+ ypos += cHeight + getAnnotationHeight() + hgap;
+
+ startRes += cWidth;
+ }
+ }
+
+ /*
+ * Draw a selection group over a wrapped alignment
+ */
+ private void drawWrappedSelection(Graphics2D g, SequenceGroup group,
+ int canvasWidth,
+ int canvasHeight, int startRes)
+ {
+ // height gap above each panel
+ int hgap = charHeight;
+ if (av.getScaleAboveWrapped())
+ {
+ hgap += charHeight;
+ }
+
+ int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / charWidth;
+ int cHeight = av.getAlignment().getHeight() * charHeight;
+
+ int startx = startRes;
+ int endx;
+ int ypos = hgap; // vertical offset
+ int maxwidth = av.getAlignment().getWidth();
+
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth);
+ }
+
+ // chop the wrapped alignment extent up into panel-sized blocks and treat
+ // each block as if it were a block from an unwrapped alignment
+ while ((ypos <= canvasHeight) && (startx < maxwidth))
+ {
+ // set end value to be start + width, or maxwidth, whichever is smaller
+ endx = startx + cWidth - 1;
+
+ if (endx > maxwidth)
+ {
+ endx = maxwidth;
+ }
+
+ g.translate(LABEL_WEST, 0);
+
+ drawUnwrappedSelection(g, group, startx, endx, 0,
+ av.getAlignment().getHeight() - 1,
+ ypos);
+
+ g.translate(-LABEL_WEST, 0);
+
+ // update vertical offset
+ ypos += cHeight + getAnnotationHeight() + hgap;
+
+ // update horizontal offset
+ startx += cWidth;
+ }
+ }
+
+ int getAnnotationHeight()
+ {
+ if (!av.isShowAnnotation())
+ {
+ return 0;
+ }
+
+ if (annotations == null)
+ {
+ annotations = new AnnotationPanel(av);
+ }
+
+ return annotations.adjustPanelHeight();
+ }
+
+ /*
+ * Draw an alignment panel for printing
+ *
+ * @param g1
+ * Graphics object to draw with
+ * @param startRes
+ * start residue of print area
+ * @param endRes
+ * end residue of print area
+ * @param startSeq
+ * start sequence of print area
+ * @param endSeq
+ * end sequence of print area
+ * @param offset
+ * vertical offset
+ */
+ private void drawPanel(Graphics g1, int startRes, int endRes,
+ int startSeq, int endSeq, int offset)
+ {
+ updateViewport();
+ if (!av.hasHiddenColumns())
+ {
+ draw(g1, startRes, endRes, startSeq, endSeq, offset);
+ }
+ else
+ {
+ int screenY = 0;
+ int blockStart = startRes;
+ int blockEnd = endRes;
+
+ for (int[] region : av.getAlignment().getHiddenColumns()
+ .getHiddenColumnsCopy())
+ {
+ int hideStart = region[0];
+ int hideEnd = region[1];
+
+ if (hideStart <= blockStart)
+ {
+ blockStart += (hideEnd - hideStart) + 1;
+ continue;
+ }
+
+ blockEnd = hideStart - 1;
+
+ g1.translate(screenY * charWidth, 0);
+
+ draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+
+ if (av.getShowHiddenMarkers())
+ {
+ g1.setColor(Color.blue);
+
+ g1.drawLine((blockEnd - blockStart + 1) * charWidth - 1,
+ 0 + offset, (blockEnd - blockStart + 1) * charWidth - 1,
+ (endSeq - startSeq + 1) * charHeight + offset);
+ }
+
+ g1.translate(-screenY * charWidth, 0);
+ screenY += blockEnd - blockStart + 1;
+ blockStart = hideEnd + 1;
+
+ if (screenY > (endRes - startRes))
+ {
+ // already rendered last block
+ return;
+ }
+ }
+
+ if (screenY <= (endRes - startRes))
+ {
+ // remaining visible region to render
+ blockEnd = blockStart + (endRes - startRes) - screenY;
+ g1.translate(screenY * charWidth, 0);
+ draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+
+ g1.translate(-screenY * charWidth, 0);
+ }
+ }
+
+ }
+
+ private void draw(Graphics g, int startRes, int endRes, int startSeq,
+ int endSeq, int offset)
+ {
+ g.setFont(av.getFont());
+ seqRdr.prepare(g, av.isRenderGaps());
+
+ SequenceI nextSeq;
+
+ // / First draw the sequences
+ // ///////////////////////////
+ for (int i = startSeq; i <= endSeq; i++)
+ {
+ nextSeq = av.getAlignment().getSequenceAt(i);
+ if (nextSeq == null)
+ {
+ // occasionally, a race condition occurs such that the alignment row is
+ // empty
+ continue;
+ }
+ seqRdr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
+ startRes, endRes, offset + ((i - startSeq) * charHeight));
+
+ if (av.isShowSequenceFeatures())
+ {
+ fr.drawSequence(g, nextSeq, startRes, endRes,
+ offset + ((i - startSeq) * charHeight), false);
+ }
+
+ // / Highlight search Results once all sequences have been drawn
+ // ////////////////////////////////////////////////////////
+ if (av.hasSearchResults())
+ {
+ int[] visibleResults = av.getSearchResults().getResults(nextSeq,
+ startRes, endRes);
+ if (visibleResults != null)
+ {
+ for (int r = 0; r < visibleResults.length; r += 2)
+ {
+ seqRdr.drawHighlightedText(nextSeq, visibleResults[r],
+ visibleResults[r + 1], (visibleResults[r] - startRes)
+ * charWidth, offset
+ + ((i - startSeq) * charHeight));
+ }
+ }
+ }
+
+ if (av.cursorMode && cursorY == i && cursorX >= startRes
+ && cursorX <= endRes)
+ {
+ seqRdr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth,
+ offset + ((i - startSeq) * charHeight));
+ }
+ }
+
+ if (av.getSelectionGroup() != null
+ || av.getAlignment().getGroups().size() > 0)
+ {
+ drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
+ }
+
+ }
+
+ void drawGroupsBoundaries(Graphics g1, int startRes, int endRes,
+ int startSeq, int endSeq, int offset)
+ {
+ Graphics2D g = (Graphics2D) g1;
+ //
+ // ///////////////////////////////////
+ // Now outline any areas if necessary
+ // ///////////////////////////////////
+
+ SequenceGroup group = null;
+ int groupIndex = -1;
+
+ if (av.getAlignment().getGroups().size() > 0)
+ {
+ group = av.getAlignment().getGroups().get(0);
+ groupIndex = 0;
+ }
+
+ if (group != null)
+ {
+ g.setStroke(new BasicStroke());
+ g.setColor(group.getOutlineColour());
+
+ do
+ {
+ drawPartialGroupOutline(g, group, startRes, endRes, startSeq,
+ endSeq, offset);
+
+ groupIndex++;
+
+ g.setStroke(new BasicStroke());
+
+ if (groupIndex >= av.getAlignment().getGroups().size())
+ {
+ break;
+ }
+
+ group = av.getAlignment().getGroups().get(groupIndex);
+
+ } while (groupIndex < av.getAlignment().getGroups().size());
+
+ }
+
+ }
+
+
+ /*
+ * Draw the selection group as a separate image and overlay
+ */
+ private BufferedImage drawSelectionGroup(int startRes, int endRes,
+ int startSeq, int endSeq)
+ {
+ // get a new image of the correct size
+ BufferedImage selectionImage = setupImage();
+
+ if (selectionImage == null)
+ {
+ return null;
+ }
+
+ SequenceGroup group = av.getSelectionGroup();
+ if (group == null)
+ {
+ // nothing to draw
+ return null;
+ }
+
+ // set up drawing colour
+ Graphics2D g = (Graphics2D) selectionImage.getGraphics();
+
+ setupSelectionGroup(g, selectionImage);
+
+ if (!av.getWrapAlignment())
+ {
+ drawUnwrappedSelection(g, group, startRes, endRes, startSeq, endSeq,
+ 0);
+ }
+ else
+ {
+ drawWrappedSelection(g, group, getWidth(), getHeight(),
+ av.getRanges().getStartRes());
+ }
+
+ g.dispose();
+ return selectionImage;
+ }
+
+ /*
+ * Set up graphics for selection group
+ */
+ private void setupSelectionGroup(Graphics2D g,
+ BufferedImage selectionImage)
+ {
+ // set background to transparent
+ g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f));
+ g.fillRect(0, 0, selectionImage.getWidth(), selectionImage.getHeight());
+
+ // set up foreground to draw red dashed line
+ g.setComposite(AlphaComposite.Src);
+ g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
+ BasicStroke.JOIN_ROUND, 3f, new float[]
+ { 5f, 3f }, 0f));
+ g.setColor(Color.RED);
+ }
+
+ /*
+ * Draw a selection group over an unwrapped alignment
+ * @param g graphics object to draw with
+ * @param group selection group
+ * @param startRes start residue of area to draw
+ * @param endRes end residue of area to draw
+ * @param startSeq start sequence of area to draw
+ * @param endSeq end sequence of area to draw
+ * @param offset vertical offset (used when called from wrapped alignment code)
+ */
+ private void drawUnwrappedSelection(Graphics2D g, SequenceGroup group,
+ int startRes, int endRes, int startSeq, int endSeq, int offset)
+ {
+ if (!av.hasHiddenColumns())
+ {
+ drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq,
+ offset);
+ }
+ else
+ {
+ // package into blocks of visible columns
+ int screenY = 0;
+ int blockStart = startRes;
+ int blockEnd = endRes;
+
+ for (int[] region : av.getAlignment().getHiddenColumns()
+ .getHiddenColumnsCopy())
+ {
+ int hideStart = region[0];
+ int hideEnd = region[1];
+
+ if (hideStart <= blockStart)
+ {
+ blockStart += (hideEnd - hideStart) + 1;
+ continue;
+ }
+
+ blockEnd = hideStart - 1;
+
+ g.translate(screenY * charWidth, 0);
+ drawPartialGroupOutline(g, group,
+ blockStart, blockEnd, startSeq, endSeq, offset);
+
+ g.translate(-screenY * charWidth, 0);
+ screenY += blockEnd - blockStart + 1;
+ blockStart = hideEnd + 1;
+
+ if (screenY > (endRes - startRes))
+ {
+ // already rendered last block
+ break;
+ }
+ }
+
+ if (screenY <= (endRes - startRes))
+ {
+ // remaining visible region to render
+ blockEnd = blockStart + (endRes - startRes) - screenY;
+ g.translate(screenY * charWidth, 0);
+ drawPartialGroupOutline(g, group,
+ blockStart, blockEnd, startSeq, endSeq, offset);
+
+ g.translate(-screenY * charWidth, 0);
+ }
+ }
+ }
+
+ /*
+ * Draw the selection group as a separate image and overlay
+ */
+ private void drawPartialGroupOutline(Graphics2D g, SequenceGroup group,
+ int startRes, int endRes, int startSeq, int endSeq,
+ int verticalOffset)
+ {
+ int visWidth = (endRes - startRes + 1) * charWidth;
+
+ int oldY = -1;
+ int i = 0;
+ boolean inGroup = false;
+ int top = -1;
+ int bottom = -1;
+
+ int sx = -1;
+ int sy = -1;
+ int xwidth = -1;
+
+ for (i = startSeq; i <= endSeq; i++)
+ {
+ // position of start residue of group relative to startRes, in pixels
+ sx = (group.getStartRes() - startRes) * charWidth;
+
+ // width of group in pixels
+ xwidth = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth)
+ - 1;
+
+ sy = verticalOffset + (i - startSeq) * charHeight;
+
+ if (sx + xwidth < 0 || sx > visWidth)
+ {
+ continue;
+ }
+
+ if ((sx <= (endRes - startRes) * charWidth)
+ && group.getSequences(null)
+ .contains(av.getAlignment().getSequenceAt(i)))
+ {
+ if ((bottom == -1) && !group.getSequences(null)
+ .contains(av.getAlignment().getSequenceAt(i + 1)))
+ {
+ bottom = sy + charHeight;
+ }
+
+ if (!inGroup)
+ {
+ if (((top == -1) && (i == 0)) || !group.getSequences(null)
+ .contains(av.getAlignment().getSequenceAt(i - 1)))
+ {
+ top = sy;
+ }
+
+ oldY = sy;
+ inGroup = true;
+ }
+ }
+ else
+ {
+ if (inGroup)
+ {
+ // if start position is visible, draw vertical line to left of
+ // group
+ if (sx >= 0 && sx < visWidth)
+ {
+ g.drawLine(sx, oldY, sx, sy);
+ }
+
+ // if end position is visible, draw vertical line to right of
+ // group
+ if (sx + xwidth < visWidth)
+ {
+ g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
+ }
+
+ if (sx < 0)
+ {
+ xwidth += sx;
+ sx = 0;
+ }
+
+ // don't let width extend beyond current block, or group extent
+ // fixes JAL-2672
+ if (sx + xwidth >= (endRes - startRes + 1) * charWidth)
+ {
+ xwidth = (endRes - startRes + 1) * charWidth - sx;
+ }
+
+ // draw horizontal line at top of group
+ if (top != -1)
+ {
+ g.drawLine(sx, top, sx + xwidth, top);
+ top = -1;
+ }
+
+ // draw horizontal line at bottom of group
+ if (bottom != -1)
+ {
+ g.drawLine(sx, bottom, sx + xwidth, bottom);
+ bottom = -1;
+ }
+
+ inGroup = false;
+ }
+ }
+ }
+
+ if (inGroup)
+ {
+ sy = verticalOffset + ((i - startSeq) * charHeight);
+ if (sx >= 0 && sx < visWidth)
+ {
+ g.drawLine(sx, oldY, sx, sy);
+ }
+
+ if (sx + xwidth < visWidth)
+ {
+ g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
+ }
+
+ if (sx < 0)
+ {
+ xwidth += sx;
+ sx = 0;
+ }
+
+ if (sx + xwidth > visWidth)
+ {
+ xwidth = visWidth;
+ }
+ else if (sx + xwidth >= (endRes - startRes + 1) * charWidth)
+ {
+ xwidth = (endRes - startRes + 1) * charWidth;
+ }
+
+ if (top != -1)
+ {
+ g.drawLine(sx, top, sx + xwidth, top);
+ top = -1;
+ }
+
+ if (bottom != -1)
+ {
+ g.drawLine(sx, bottom - 1, sx + xwidth, bottom - 1);
+ bottom = -1;
+ }
+
+ inGroup = false;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param results
+ * DOCUMENT ME!
+ */
+ public void highlightSearchResults(SearchResultsI results)
+ {
+ img = null;
+
+ av.setSearchResults(results);
+
+ repaint();
+ }
+
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ String eventName = evt.getPropertyName();
+
+ if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED))
+ {
+ fastPaint = true;
+ repaint();
+ }
+ else if (av.getWrapAlignment())
+ {
+ if (eventName.equals(ViewportRanges.STARTRES))
+ {
+ repaint();
+ }
+ }
+ else
+ {
+ int scrollX = 0;
+ if (eventName.equals(ViewportRanges.STARTRES))
+ {
+ // Make sure we're not trying to draw a panel
+ // larger than the visible window
+ ViewportRanges vpRanges = av.getRanges();
+ scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
+ int range = vpRanges.getEndRes() - vpRanges.getStartRes();
+ if (scrollX > range)
+ {
+ scrollX = range;
+ }
+ else if (scrollX < -range)
+ {
+ scrollX = -range;
+ }
+ }
+
+ // Both scrolling and resizing change viewport ranges: scrolling changes
+ // both start and end points, but resize only changes end values.
+ // Here we only want to fastpaint on a scroll, with resize using a normal
+ // paint, so scroll events are identified as changes to the horizontal or
+ // vertical start value.
+ if (eventName.equals(ViewportRanges.STARTRES))
+ {
+ // scroll - startres and endres both change
+ fastPaint(scrollX, 0);
+ }
+ else if (eventName.equals(ViewportRanges.STARTSEQ))
+ {
+ // scroll
+ fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
+ }
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff