X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=eedb3eb87d92785c2c77487d4891c4d0ac19d718;hb=6de402db90987d3645f3429d9073c13678d8e980;hp=2f02d5793091599b7cd26835c8f6a10925771a32;hpb=f1b17730086767d55e4f5fea54b72e4d30d52e65;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 2f02d57..eedb3eb 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -1,184 +1,303 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program 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 2 + * of the License, or (at your option) any later version. + * + * This program 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 this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ package jalview.gui; import java.awt.*; import java.awt.image.*; import javax.swing.*; -import jalview.datamodel.*; -import jalview.analysis.*; +import jalview.datamodel.*; -public class SeqCanvas extends JComponent +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class SeqCanvas + extends JComponent { - FeatureRenderer fr; - SequenceRenderer sr; - BufferedImage img; - Graphics2D gg; - int imgWidth; - int imgHeight; - - AlignViewport av; - - boolean showScores = false; - boolean displaySearch = false; - int [] searchResults = null; - - int chunkHeight; - int chunkWidth; - - boolean fastPaint = false; + final FeatureRenderer fr; + final SequenceRenderer sr; + BufferedImage img; + Graphics2D gg; + int imgWidth; + int imgHeight; + AlignViewport av; + SearchResults searchResults = null; + boolean fastPaint = false; + int LABEL_WEST; + int LABEL_EAST; + + int cursorX = 0; + int cursorY = 0; + + /** + * Creates a new SeqCanvas object. + * + * @param av DOCUMENT ME! + */ + public SeqCanvas(AlignmentPanel ap) + { + this.av = ap.av; + fr = new FeatureRenderer(ap); + sr = new SequenceRenderer(av); + setLayout(new BorderLayout()); + PaintRefresher.Register(this, av.getSequenceSetId()); + setBackground(Color.white); + } + public SequenceRenderer getSequenceRenderer() + { + return sr; + } - public SeqCanvas(AlignViewport av) - { - this.av = av; - fr = new FeatureRenderer(av); - sr = new SequenceRenderer(av); - setLayout(new BorderLayout()); - PaintRefresher.Register(this); + public FeatureRenderer getFeatureRenderer() + { + return fr; + } - } - void drawNorthScale(Graphics g, int startx, int endx,int ypos) { - int scalestartx = startx - startx % 10 + 10; + /** + * DOCUMENT ME! + * + * @param g DOCUMENT ME! + * @param startx DOCUMENT ME! + * @param endx DOCUMENT ME! + * @param ypos DOCUMENT ME! + */ + void drawNorthScale(Graphics g, int startx, int endx, int ypos) + { + int scalestartx = startx - (startx % 10) + 10; g.setColor(Color.black); // NORTH SCALE for (int i = scalestartx; i < endx; i += 10) { - String string = String.valueOf(i); - g.drawString(string, (i - startx - 1) * av.charWidth, - ypos - av.charHeight / 2); + int value = i; + if (av.hasHiddenColumns) + { + value = av.getColumnSelection().adjustForHiddenColumns(value); + } - g.drawLine( (i - startx - 1) * av.charWidth + av.charWidth / 2, - ypos + 2 - av.charHeight / 2, - (i - startx - 1) * av.charWidth + av.charWidth / 2, ypos - 2); + g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth, + ypos - (av.charHeight / 2)); + g.drawLine( ( (i - startx - 1) * av.charWidth) + (av.charWidth / 2), + (ypos + 2) - (av.charHeight / 2), + ( (i - startx - 1) * av.charWidth) + (av.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+= av.charHeight; - // EAST SCALE + ypos += av.charHeight; + + if (av.hasHiddenColumns) + { + startx = av.getColumnSelection().adjustForHiddenColumns(startx); + endx = av.getColumnSelection().adjustForHiddenColumns(endx); + } + + int maxwidth = av.alignment.getWidth(); + if (av.hasHiddenColumns) + { + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + } + + // WEST SCALE for (int i = 0; i < av.alignment.getHeight(); i++) { SequenceI seq = av.alignment.getSequenceAt(i); int index = startx; int value = -1; + while (index < endx) { if (jalview.util.Comparison.isGap(seq.getCharAt(index))) { index++; + continue; } value = av.alignment.getSequenceAt(i).findPosition(index); + break; } - if(value!=-1) + + if (value != -1) { - int x = LABEL_WEST - fm.stringWidth(value+""); - g.drawString(value + "", x, ypos + i*av.charHeight - av.charHeight/5); + int x = LABEL_WEST - fm.stringWidth(String.valueOf(value)) - + av.charWidth / 2; + g.drawString(value + "", x, + (ypos + (i * av.charHeight)) - (av.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+= av.charHeight; - // EAST SCALE - for (int i = 0; i < av.alignment.getHeight(); i++) { - SequenceI seq = av.alignment.getSequenceAt(i); - int index = endx; - int value = -1; - while (index > startx) - { - if (jalview.util.Comparison.isGap(seq.getCharAt(index))) - { - index--; - continue; - } + ypos += av.charHeight; - value = av.alignment.getSequenceAt(i).findPosition(index); - break; + if (av.hasHiddenColumns) + { + endx = av.getColumnSelection().adjustForHiddenColumns(endx); } - if(value!=-1) - g.drawString(value + "", 0, ypos + i*av.charHeight - av.charHeight/5); - } -} + SequenceI seq; + // EAST SCALE + for (int i = 0; i < av.alignment.getHeight(); i++) + { + seq = av.alignment.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; + } -public void fastPaint(int horizontal, int vertical) -{ - if (horizontal == 0 && vertical == 0 || gg==null) + if (value != -1) + { + g.drawString(String.valueOf(value), 0, + (ypos + (i * av.charHeight)) - (av.charHeight / 5)); + } + } + } + + /** + * DOCUMENT ME! + * + * @param horizontal DOCUMENT ME! + * @param vertical DOCUMENT ME! + */ + public void fastPaint(int horizontal, int vertical) + { + if (gg == null) + { return; + } - gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth, + fastPaint = true; + + gg.copyArea(horizontal * av.charWidth, + vertical * av.charHeight, + imgWidth, + imgHeight, + -horizontal * av.charWidth, -vertical * av.charHeight); - int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, - transX = 0, transY = 0; + int sr = av.startRes; + int er = av.endRes; + int ss = av.startSeq; + int es = av.endSeq; + int transX = 0; + int transY = 0; + if (horizontal > 0) // scrollbar pulled right, image to the left { + er++; transX = (er - sr - horizontal) * av.charWidth; sr = er - horizontal; } else if (horizontal < 0) - er = sr - horizontal; - + { + er = sr - horizontal - 1; + } else if (vertical > 0) // scroll down { ss = es - vertical; - if(ss av.endSeq) + + if (es > av.endSeq) + { es = av.endSeq; + } } - gg.translate(transX, transY); - - gg.setColor(Color.white); - gg.fillRect(0,0, (er-sr+1)*av.charWidth, (es-ss)*av.charHeight); - drawPanel(gg, sr, er, ss, es, sr, ss, 0); + drawPanel(gg, sr, er, ss, es, 0); gg.translate( -transX, -transY); - fastPaint = true; repaint(); + } -} - -/** - * 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. - */ - - public void paint(Graphics g) + /** + * 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 + public void paintComponent(Graphics g) { - g.setColor(Color.white); - g.fillRect(0, 0, getWidth(), getHeight()); + super.paintComponent(g); - if (fastPaint) + if (img != null && (fastPaint + || (getVisibleRect().width != g.getClipBounds().width) + || (getVisibleRect().height != g.getClipBounds().height))) { g.drawImage(img, 0, 0, this); fastPaint = false; @@ -186,39 +305,78 @@ public void fastPaint(int horizontal, int vertical) } // this draws the whole of the alignment - imgWidth = getWidth(); - imgHeight = getHeight(); - if(imgWidth<0 || imgHeight<1) - return; + imgWidth = getWidth(); + imgHeight = getHeight(); - imgWidth -= imgWidth%av.charWidth; - imgHeight-= imgHeight%av.charHeight; + imgWidth -= (imgWidth % av.charWidth); + imgHeight -= (imgHeight % av.charHeight); - img = new BufferedImage(imgWidth,imgHeight,BufferedImage.TYPE_INT_RGB); - gg = (Graphics2D)img.getGraphics(); - gg.setFont(av.getFont()); - gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON); + if ( (imgWidth < 1) || (imgHeight < 1)) + { + return; + } - gg.setColor(Color.white); - gg.fillRect(0,0,imgWidth,imgHeight); + if (img == null || imgWidth != img.getWidth() || imgHeight != img.getHeight()) + { + try + { + img = new BufferedImage(imgWidth, imgHeight, + BufferedImage.TYPE_INT_RGB); + gg = (Graphics2D) img.getGraphics(); + gg.setFont(av.getFont()); + } + catch (OutOfMemoryError er) + { + System.gc(); + System.out.println(er + " making image, SeqCanvas"); + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + javax.swing.JOptionPane.showInternalMessageDialog(Desktop. + desktop, + "Out of memory creating alignment image!!" + + + "\nSee help files for increasing Java Virtual Machine memory." + , "Out of memory", + javax.swing.JOptionPane.WARNING_MESSAGE); + } + }); - chunkWidth = getWrappedCanvasWidth( getWidth() ); - chunkHeight = (av.getAlignment().getHeight() + 2)*av.charHeight; + return; + } + } - av.setChunkHeight(chunkHeight); - av.setChunkWidth(chunkWidth); + if (av.antiAlias) + { + gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); + } + gg.setColor(Color.white); + gg.fillRect(0, 0, imgWidth, imgHeight); if (av.getWrapAlignment()) + { drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes); + } else - drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes, av.startSeq, 0); + { + drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0); + } g.drawImage(img, 0, 0, this); + } - int LABEL_WEST, LABEL_EAST; + /** + * DOCUMENT ME! + * + * @param cwidth DOCUMENT ME! + * + * @return DOCUMENT ME! + */ public int getWrappedCanvasWidth(int cwidth) { FontMetrics fm = getFontMetrics(av.getFont()); @@ -226,161 +384,412 @@ public void fastPaint(int horizontal, int vertical) LABEL_EAST = 0; LABEL_WEST = 0; - if(av.scaleRightWrapped) - LABEL_EAST = fm.stringWidth( av.alignment.getWidth()+"000" ); + if (av.scaleRightWrapped) + { + LABEL_EAST = fm.stringWidth(getMask()); + } - if(av.scaleLeftWrapped) - LABEL_WEST = fm.stringWidth( av.alignment.getWidth()+"" ); + if (av.scaleLeftWrapped) + { + LABEL_WEST = fm.stringWidth(getMask()); + } - return (cwidth - LABEL_EAST -LABEL_WEST)/av.charWidth; + return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth; } - public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes) + /** + * Generates a string of zeroes. + * @return String + */ + String getMask() { - AlignmentI al = av.getAlignment(); + String mask = "00"; + int maxWidth = 0; + int tmp; + for (int i = 0; i < av.alignment.getHeight(); i++) + { + tmp = av.alignment.getSequenceAt(i).getEnd(); + if (tmp > maxWidth) + { + maxWidth = tmp; + } + } + + for (int i = maxWidth; i > 0; i /= 10) + { + mask += "0"; + } + return mask; + } - FontMetrics fm = getFontMetrics(av.getFont()); + /** + * DOCUMENT ME! + * + * @param g DOCUMENT ME! + * @param canvasWidth DOCUMENT ME! + * @param canvasHeight DOCUMENT ME! + * @param startRes DOCUMENT ME! + */ + public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, + int startRes) + { + AlignmentI al = av.getAlignment(); - int LABEL_EAST = 0; - if(av.scaleRightWrapped) - LABEL_EAST = fm.stringWidth( al.getWidth()+"000" ); - int LABEL_WEST = 0; - if(av.scaleLeftWrapped) - LABEL_WEST = fm.stringWidth(al.getWidth()+"0"); + FontMetrics fm = getFontMetrics(av.getFont()); + if (av.scaleRightWrapped) + { + LABEL_EAST = fm.stringWidth(getMask()); + } - int cWidth = (canvasWidth - LABEL_EAST -LABEL_WEST)/av.charWidth; - int cHeight = (av.getAlignment().getHeight() + 2)*av.charHeight; + if (av.scaleLeftWrapped) + { + LABEL_WEST = fm.stringWidth(getMask()); + } + + int hgap = av.charHeight; + if (av.scaleAboveWrapped) + { + hgap += av.charHeight; + } - av.endRes = av.startRes + cWidth; + int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth; + int cHeight = av.getAlignment().getHeight() * av.charHeight; - int endx = startRes+cWidth-1; - int ypos = 2*av.charHeight; + av.setWrappedWidth(cWidth); - while (ypos <= canvasHeight && startRes maxwidth) { - g.setColor(Color.black); + endx = maxwidth; + } - if(av.scaleLeftWrapped) - drawWestScale(g, startRes, endx, ypos); + g.setFont(av.getFont()); + g.setColor(Color.black); - if(av.scaleRightWrapped) + if (av.scaleLeftWrapped) + { + drawWestScale(g, startRes, endx, ypos); + } + + if (av.scaleRightWrapped) + { + g.translate(canvasWidth - LABEL_EAST, 0); + drawEastScale(g, startRes, endx, ypos); + g.translate( - (canvasWidth - LABEL_EAST), 0); + } + + g.translate(LABEL_WEST, 0); + + if (av.scaleAboveWrapped) + { + drawNorthScale(g, startRes, endx, ypos); + } + + if (av.hasHiddenColumns && av.showHiddenMarkers) + { + g.setColor(Color.blue); + int res; + for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); + i++) + { + res = av.getColumnSelection().findHiddenRegionPosition(i) - + startRes; + + if (res < 0 || res > endx - startRes) + { + continue; + } + + gg.fillPolygon(new int[] + {res * av.charWidth - av.charHeight / 4, + res * av.charWidth + av.charHeight / 4, + res * av.charWidth}, + new int[] + { + ypos - (av.charHeight / 2), + ypos - (av.charHeight / 2), + ypos - (av.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 * av.charWidth, canvasHeight); + } + else + { + g.setClip(0, (int) clip.getBounds().getY(), + cWidth * av.charWidth, (int) clip.getBounds().getHeight()); + } + + drawPanel(g, startRes, endx, 0, al.getHeight(), ypos); + + if (av.showAnnotation) + { + g.translate(0, cHeight + ypos + 3); + if (annotations == null) { - g.translate(canvasWidth - LABEL_EAST +av.charWidth, 0); - drawEastScale(g, startRes, endx, ypos); - g.translate( - (canvasWidth - LABEL_EAST+av.charWidth), 0); + annotations = new AnnotationPanel(av); } - g.translate(LABEL_WEST,0); - if(av.scaleAboveWrapped) - drawNorthScale(g, startRes, endx, ypos); - - - // 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*av.charWidth, canvasHeight); - else - g.setClip(0, - (int)clip.getBounds().getY(), - cWidth*av.charWidth, - (int)clip.getBounds().getHeight() - ); - - drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos); - g.setClip(clip); - g.translate(-LABEL_WEST,0); - - ypos += cHeight; - startRes += cWidth; - endx = startRes + cWidth - 1; - - if (endx > al.getWidth()) - endx = al.getWidth(); + annotations.drawComponent( (Graphics2D) g, startRes, endx + 1); + g.translate(0, -cHeight - ypos - 3); } + g.setClip(clip); + g.translate( -LABEL_WEST, 0); + + ypos += cHeight + getAnnotationHeight() + hgap; + startRes += cWidth; + } } + AnnotationPanel annotations; + int getAnnotationHeight() + { + if (!av.showAnnotation) + { + return 0; + } + + if (annotations == null) + { + annotations = new AnnotationPanel(av); + } - synchronized public void drawPanel(Graphics g1,int x1,int x2, int y1, int y2,int startx, int starty,int offset) { + return annotations.adjustPanelHeight(); + } - Graphics2D g = (Graphics2D)g1; - g.setFont(av.getFont()); - sr.renderGaps(av.renderGaps); + /** + * DOCUMENT ME! + * + * @param g1 DOCUMENT ME! + * @param startRes DOCUMENT ME! + * @param endRes DOCUMENT ME! + * @param startSeq DOCUMENT ME! + * @param endSeq DOCUMENT ME! + * @param offset DOCUMENT ME! + */ + void drawPanel(Graphics g1, int startRes, int endRes, + int startSeq, int endSeq, int offset) + { + if (!av.hasHiddenColumns) + { + draw(g1, startRes, endRes, startSeq, endSeq, offset); + } + else + { + java.util.Vector regions = av.getColumnSelection().getHiddenColumns(); + int screenY = 0; + int blockStart = startRes; + int blockEnd = endRes; + + for (int i = 0; i < regions.size(); i++) + { + int[] region = (int[]) regions.elementAt(i); + int hideStart = region[0]; + int hideEnd = region[1]; + + if (hideStart <= blockStart) + { + blockStart += (hideEnd - hideStart) + 1; + continue; + } + + blockEnd = hideStart - 1; + + g1.translate(screenY * av.charWidth, 0); + + draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); + + if (av.getShowHiddenMarkers()) + { + g1.setColor(Color.blue); + + g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1, + 0 + offset, + (blockEnd - blockStart + 1) * av.charWidth - 1, + (endSeq - startSeq) * av.charHeight + offset); + } + + g1.translate( -screenY * av.charWidth, 0); + screenY += blockEnd - blockStart + 1; + blockStart = hideEnd + 1; + } + + if (screenY <= (endRes - startRes)) + { + blockEnd = blockStart + (endRes - startRes) - screenY; + g1.translate(screenY * av.charWidth, 0); + draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); + + g1.translate( -screenY * av.charWidth, 0); + } + } + + } + + //int startRes, int endRes, int startSeq, int endSeq, int x, int y, + // int x1, int x2, int y1, int y2, int startx, int starty, + void draw(Graphics g, + int startRes, int endRes, + int startSeq, int endSeq, + int offset) + { + g.setFont(av.getFont()); + sr.prepare(g, av.renderGaps); SequenceI nextSeq; /// First draw the sequences ///////////////////////////// - for (int i = y1 ; i < y2 ;i++) + for (int i = startSeq; i < endSeq; i++) { - nextSeq = av.alignment.getSequenceAt(i); + nextSeq = av.alignment.getSequenceAt(i); + + sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq), + startRes, endRes, + offset + ( (i - startSeq) * av.charHeight)); + + if (av.showSequenceFeatures) + { + fr.drawSequence(g, nextSeq, startRes, endRes, + offset + ( (i - startSeq) * av.charHeight)); + } + + /// Highlight search Results once all sequences have been drawn + ////////////////////////////////////////////////////////// + if (searchResults != null) + { + int[] visibleResults = searchResults.getResults(nextSeq, startRes, + endRes); + if (visibleResults != null) + { + for (int r = 0; r < visibleResults.length; r += 2) + { + sr.drawHighlightedText(nextSeq, visibleResults[r], + visibleResults[r + 1], + (visibleResults[r] - startRes) * + av.charWidth, + offset + ( (i - startSeq) * av.charHeight)); + } + } + } - sr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ),x1,x2, - (x1 - startx) * av.charWidth, - offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight), - av.charWidth,av.charHeight); + if (av.cursorMode && cursorY == i + && cursorX >= startRes && cursorX <= endRes) + { + sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * av.charWidth, + offset + ( (i - startSeq) * av.charHeight)); + } + } - if(av.showSequenceFeatures) - { - fr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ), x1, x2, - (x1 - startx) * av.charWidth, - offset + - AlignmentUtil.getPixelHeight(starty, i, av.charHeight), - av.charWidth, av.charHeight); - } + if (av.getSelectionGroup() != null || av.alignment.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 = av.getSelectionGroup(); - java.util.Vector groups = av.alignment.getGroups(); - int sx = -1, sy = -1, ex = -1; + int sx = -1; + int sy = -1; + int ex = -1; int groupIndex = -1; - if (group == null && groups.size() > 0) + int visWidth = (endRes - startRes + 1) * av.charWidth; + + if ( (group == null) && (av.alignment.getGroups().size() > 0)) { - group = (SequenceGroup) groups.elementAt(0); + group = (SequenceGroup) av.alignment.getGroups().elementAt(0); groupIndex = 0; } if (group != null) + { do { int oldY = -1; int i = 0; boolean inGroup = false; - int top=-1, bottom =-1; - for (i = y1; i < y2; i++) + int top = -1; + int bottom = -1; + + for (i = startSeq; i < endSeq; i++) { - sx = (group.getStartRes() - startx) * av.charWidth; - sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight); - ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth -1; + sx = (group.getStartRes() - startRes) * av.charWidth; + sy = offset + ( (i - startSeq) * av.charHeight); + ex = ( ( (group.getEndRes() + 1) - group.getStartRes()) * + av.charWidth) - + 1; - if (sx < getWidth() - && ex > 0 - && group.sequences.contains(av.alignment.getSequenceAt(i))) + if (sx + ex < 0 || sx > visWidth) { - if (bottom == -1 && - !group.sequences.contains(av.alignment.getSequenceAt(i + 1))) - bottom = sy + av.charHeight ; + continue; + } + + if ( (sx <= (endRes - startRes) * av.charWidth) && + group.getSequences(null). + contains(av.alignment.getSequenceAt(i))) + { + if ( (bottom == -1) && + !group.getSequences(null).contains( + av.alignment.getSequenceAt(i + 1))) + { + bottom = sy + av.charHeight; + } if (!inGroup) { - if (top == -1 && i==0 || - !group.sequences.contains(av.alignment.getSequenceAt(i - 1))) + if ( ( (top == -1) && (i == 0)) || + !group.getSequences(null).contains( + av.alignment.getSequenceAt(i - 1))) + { top = sy; - + } oldY = sy; inGroup = true; + if (group == av.getSelectionGroup()) { - g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND, 3f, new float[]{5f,3f}, 0f )); + g.setStroke(new BasicStroke(1, + BasicStroke.CAP_BUTT, + BasicStroke.JOIN_ROUND, 3f, + new float[] + {5f, 3f}, 0f)); g.setColor(Color.RED); } else @@ -394,21 +803,44 @@ public void fastPaint(int horizontal, int vertical) { if (inGroup) { - g.drawLine(sx, oldY, sx, sy ); - g.drawLine(sx+ex, oldY, sx+ex, sy ); + if (sx >= 0 && sx < visWidth) + { + g.drawLine(sx, oldY, sx, sy); + } + + if (sx + ex < visWidth) + { + g.drawLine(sx + ex, oldY, sx + ex, sy); + } + + if (sx < 0) + { + ex += sx; + sx = 0; + } + + if (sx + ex > visWidth) + { + ex = visWidth; + } + + else if (sx + ex >= (endRes - startRes + 1) * av.charWidth) + { + ex = (endRes - startRes + 1) * av.charWidth; + } if (top != -1) { g.drawLine(sx, top, sx + ex, top); - top =-1; + top = -1; } + if (bottom != -1) { g.drawLine(sx, bottom, sx + ex, bottom); bottom = -1; } - inGroup = false; } } @@ -416,79 +848,76 @@ public void fastPaint(int horizontal, int vertical) if (inGroup) { + sy = offset + ( (i - startSeq) * av.charHeight); + if (sx >= 0 && sx < visWidth) + { + g.drawLine(sx, oldY, sx, sy); + } + + if (sx + ex < visWidth) + { + g.drawLine(sx + ex, oldY, sx + ex, sy); + } + + if (sx < 0) + { + ex += sx; + sx = 0; + } - if(top!=-1) + if (sx + ex > visWidth) + { + ex = visWidth; + } + else if (sx + ex >= (endRes - startRes + 1) * av.charWidth) + { + ex = (endRes - startRes + 1) * av.charWidth; + } + + if (top != -1) { g.drawLine(sx, top, sx + ex, top); - top =-1; + top = -1; } - if(bottom!=-1) - { - g.drawLine(sx, bottom-1, sx + ex, bottom-1); - bottom = -1; - - } - sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight); - g.drawLine(sx, oldY, sx, sy ); - g.drawLine(sx+ex, oldY, sx+ex, sy ); - inGroup = false; - } - groupIndex++; - if (groupIndex >= groups.size()) - break; - group = (SequenceGroup) groups.elementAt(groupIndex); + if (bottom != -1) + { + g.drawLine(sx, bottom - 1, sx + ex, bottom - 1); + bottom = -1; + } - } - while (groupIndex < groups.size()); + inGroup = false; + } + groupIndex++; - /// Highlight search Results once all sequences have been drawn - ////////////////////////////////////////////////////////// - if(displaySearch) - { - for(int r=0; r= y1 && searchSeq < y2) + if (groupIndex >= av.alignment.getGroups().size()) { - SequenceRenderer ssr = (SequenceRenderer) sr; - if(searchStart x2) - searchEnd = x2; - ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq), - searchStart, - searchEnd, - (searchStart - startx) * av.charWidth, - offset + - AlignmentUtil.getPixelHeight(starty, searchSeq, - av.charHeight), - av.charWidth, - av.charHeight); + break; } + + group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex); + } + while (groupIndex < av.alignment.getGroups().size()); + } } - - - public void highlightSearchResults(int [] results) + /** + * DOCUMENT ME! + * + * @param results DOCUMENT ME! + */ + public void highlightSearchResults(SearchResults results) { - // results are in the order sequence, startRes, endRes - if(results==null) - displaySearch = false; - else - displaySearch = true; + img = null; searchResults = results; repaint(); } - - }