X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=438d7ad7d69019f61de55860eac831b77c1198cf;hb=588042b69abf8e60bcc950b24c283933c7dd422f;hp=6855468016e5c448132459efd9a19a9b6ad84c68;hpb=5cd8e373c75fb348ecda4d94d8a46468fb92756d;p=jalview.git diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java index 6855468..438d7ad 100755 --- a/src/jalview/appletgui/SeqCanvas.java +++ b/src/jalview/appletgui/SeqCanvas.java @@ -1,60 +1,61 @@ /* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 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 -*/ + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2005 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.appletgui; import java.awt.*; -import jalview.datamodel.*; -import jalview.analysis.*; +import jalview.analysis.*; +import jalview.datamodel.*; -public class SeqCanvas extends Panel +public class SeqCanvas + extends Panel { - FeatureRenderer fr; - SequenceRenderer sr; - Image img; - Graphics gg; - int imgWidth; - int imgHeight; - - AlignViewport av; + FeatureRenderer fr; + SequenceRenderer sr; + Image img; + Graphics gg; + int imgWidth; + int imgHeight; - boolean showScores = false; - boolean displaySearch = false; - int [] searchResults = null; + AlignViewport av; - int chunkHeight; - int chunkWidth; + boolean showScores = false; + boolean displaySearch = false; + int[] searchResults = null; - boolean fastPaint = false; + int chunkHeight; + int chunkWidth; + boolean fastPaint = false; - public SeqCanvas(AlignViewport av) - { - this.av = av; - fr = new FeatureRenderer(av); - sr = new SequenceRenderer(av); - PaintRefresher.Register(this); + public SeqCanvas(AlignViewport av) + { + this.av = av; + fr = new FeatureRenderer(av); + sr = new SequenceRenderer(av); + PaintRefresher.Register(this); - } + } - void drawNorthScale(Graphics g, int startx, int endx,int ypos) { + void drawNorthScale(Graphics g, int startx, int endx, int ypos) + { int scalestartx = startx - startx % 10 + 10; g.setColor(Color.black); @@ -76,8 +77,8 @@ public class SeqCanvas extends Panel void drawWestScale(Graphics g, int startx, int endx, int ypos) { FontMetrics fm = getFontMetrics(av.getFont()); - ypos+= av.charHeight; - // EAST SCALE + ypos += av.charHeight; + // EAST SCALE for (int i = 0; i < av.alignment.getHeight(); i++) { SequenceI seq = av.alignment.getSequenceAt(i); @@ -94,46 +95,50 @@ public class SeqCanvas extends Panel 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(value + ""); + g.drawString(value + "", x, + ypos + i * av.charHeight - av.charHeight / 5); } } } 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) + ypos += av.charHeight; + // EAST SCALE + for (int i = 0; i < av.alignment.getHeight(); i++) { - if (jalview.util.Comparison.isGap(seq.getCharAt(index))) + SequenceI seq = av.alignment.getSequenceAt(i); + int index = endx; + int value = -1; + while (index > startx) { - index--; - continue; - } + if (jalview.util.Comparison.isGap(seq.getCharAt(index))) + { + index--; + continue; + } - value = av.alignment.getSequenceAt(i).findPosition(index); - break; + value = av.alignment.getSequenceAt(i).findPosition(index); + break; + } + if (value != -1) + { + g.drawString(value + "", 0, + ypos + i * av.charHeight - av.charHeight / 5); + } } - if(value!=-1) - g.drawString(value + "", 0, ypos + i*av.charHeight - av.charHeight/5); - } - -} - + } -public void fastPaint(int horizontal, int vertical) -{ - if (horizontal == 0 && vertical == 0 || gg==null) + public void fastPaint(int horizontal, int vertical) + { + if (horizontal == 0 && vertical == 0 || gg == null) + { return; + } gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth, -vertical * av.charHeight); @@ -146,46 +151,53 @@ public void fastPaint(int horizontal, int vertical) sr = er - horizontal; } else if (horizontal < 0) + { er = sr - horizontal; + } 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); + gg.fillRect(0, 0, (er - sr + 1) * av.charWidth, (es - ss) * av.charHeight); drawPanel(gg, sr, er, ss, es, sr, ss, 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. - */ + /** + * 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 update(Graphics g) { paint(g); @@ -201,36 +213,43 @@ public void fastPaint(int horizontal, int vertical) } // this draws the whole of the alignment - imgWidth = this.getSize().width; - imgHeight = this.getSize().height; + imgWidth = this.getSize().width; + imgHeight = this.getSize().height; - imgWidth -= imgWidth%av.charWidth; - imgHeight-= imgHeight%av.charHeight; + imgWidth -= imgWidth % av.charWidth; + imgHeight -= imgHeight % av.charHeight; - if(imgWidth<1 || imgHeight<1) - return; + if (imgWidth < 1 || imgHeight < 1) + { + return; + } - if(img==null || imgWidth!=img.getWidth(this) || imgHeight!=img.getHeight(this)) - { - img = createImage(imgWidth, imgHeight); - gg = img.getGraphics(); - gg.setFont(av.getFont()); - } + if (img == null || imgWidth != img.getWidth(this) || + imgHeight != img.getHeight(this)) + { + img = createImage(imgWidth, imgHeight); + gg = img.getGraphics(); + gg.setFont(av.getFont()); + } - gg.setColor(Color.white); - gg.fillRect(0,0,imgWidth,imgHeight); + gg.setColor(Color.white); + gg.fillRect(0, 0, imgWidth, imgHeight); - chunkWidth = getWrappedCanvasWidth( getSize().width ); - chunkHeight = (av.getAlignment().getHeight() + 2)*av.charHeight; + chunkWidth = getWrappedCanvasWidth(getSize().width); + chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight; av.setChunkHeight(chunkHeight); av.setChunkWidth(chunkWidth); - if (av.getWrapAlignment()) + { drawWrappedPanel(gg, getSize().width, getSize().height, 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, av.startRes, + av.startSeq, 0); + } g.drawImage(img, 0, 0, this); @@ -244,84 +263,102 @@ 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(av.alignment.getWidth() + "000"); + } - if(av.scaleLeftWrapped) - LABEL_WEST = fm.stringWidth( av.alignment.getWidth()+"" ); + if (av.scaleLeftWrapped) + { + LABEL_WEST = fm.stringWidth(av.alignment.getWidth() + ""); + } - 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) + public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, + int startRes) { - AlignmentI al = av.getAlignment(); + AlignmentI al = av.getAlignment(); - FontMetrics fm = getFontMetrics(av.getFont()); + FontMetrics fm = getFontMetrics(av.getFont()); - 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"); + 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"); + } + int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth; + int cHeight = (av.getAlignment().getHeight() + 2) * av.charHeight; - int cWidth = (canvasWidth - LABEL_EAST -LABEL_WEST)/av.charWidth; - int cHeight = (av.getAlignment().getHeight() + 2)*av.charHeight; + av.endRes = av.startRes + cWidth; - av.endRes = av.startRes + cWidth; + int endx = startRes + cWidth - 1; + int ypos = 2 * av.charHeight; - int endx = startRes+cWidth-1; - int ypos = 2*av.charHeight; + while (ypos <= canvasHeight && startRes < av.alignment.getWidth()) + { + g.setColor(Color.black); - while (ypos <= canvasHeight && startRes al.getWidth()) - endx = al.getWidth(); + // 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().y, + cWidth * av.charWidth, + (int) clip.getBounds().height + ); } - } + 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; - synchronized public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) { + if (endx > al.getWidth()) + { + endx = al.getWidth(); + } + } + + } + + synchronized public void drawPanel(Graphics g, int x1, int x2, int y1, int y2, + int startx, int starty, int offset) + { g.setFont(av.getFont()); sr.renderGaps(av.renderGaps); @@ -330,23 +367,24 @@ public void fastPaint(int horizontal, int vertical) /// First draw the sequences ///////////////////////////// - for (int i = y1 ; i < y2 ;i++) + for (int i = y1; i < y2; i++) { - nextSeq = av.alignment.getSequenceAt(i); - - 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.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); - } + nextSeq = av.alignment.getSequenceAt(i); + + 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.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); + } } // ///////////////////////////////////// @@ -365,42 +403,47 @@ public void fastPaint(int horizontal, int vertical) } if (group != null) + { do { int oldY = -1; int i = 0; boolean inGroup = false; - int top=-1, bottom =-1; + int top = -1, bottom = -1; for (i = y1; i < y2; i++) { sx = (group.getStartRes() - startx) * av.charWidth; sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight); - ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth -1; + ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth - 1; if (sx < getSize().width && ex > 0 && group.sequences.contains(av.alignment.getSequenceAt(i))) { - if (bottom == -1 && (i==av.alignment.getHeight()-1 || - !group.sequences.contains(av.alignment.getSequenceAt(i + 1)))) - bottom = sy + av.charHeight ; + if (bottom == -1 && (i == av.alignment.getHeight() - 1 || + !group.sequences.contains(av.alignment. + getSequenceAt(i + 1)))) + { + bottom = sy + av.charHeight; + } if (!inGroup) { - if (top == -1 && i==0 || + if (top == -1 && i == 0 || !group.sequences.contains(av.alignment.getSequenceAt(i - 1))) + { top = sy; - + } oldY = sy; inGroup = true; if (group == av.getSelectionGroup()) { - g.setColor(new Color(255,0,0)); + g.setColor(new Color(255, 0, 0)); } else { - g.setColor(group.getOutlineColour()); + g.setColor(group.getOutlineColour()); } } } @@ -408,13 +451,13 @@ public void fastPaint(int horizontal, int vertical) { if (inGroup) { - g.drawLine(sx, oldY, sx, sy ); - g.drawLine(sx+ex, oldY, sx+ex, sy ); + g.drawLine(sx, oldY, sx, sy); + g.drawLine(sx + ex, oldY, sx + ex, sy); if (top != -1) { g.drawLine(sx, top, sx + ex, top); - top =-1; + top = -1; } if (bottom != -1) { @@ -422,7 +465,6 @@ public void fastPaint(int horizontal, int vertical) bottom = -1; } - inGroup = false; } } @@ -431,37 +473,39 @@ public void fastPaint(int horizontal, int vertical) if (inGroup) { - if(top!=-1) + 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; + 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 ); + 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); } while (groupIndex < groups.size()); - + } /// Highlight search Results once all sequences have been drawn ////////////////////////////////////////////////////////// - if(displaySearch) + if (displaySearch) { - for(int r=0; r x2) + } + if (searchEnd > x2) + { searchEnd = x2; + } ssr.drawHighlightedText(seq, searchStart, searchEnd, (searchStart - startx) * av.charWidth, offset + - AlignmentUtil.getPixelHeight(starty, searchSeq, + AlignmentUtil.getPixelHeight(starty, + searchSeq, av.charHeight), av.charWidth, av.charHeight); @@ -493,20 +542,21 @@ public void fastPaint(int horizontal, int vertical) } - - - public void highlightSearchResults(int [] results) + public void highlightSearchResults(int[] results) { // results are in the order sequence, startRes, endRes - if(results==null) + if (results == null) + { displaySearch = false; + } else + { displaySearch = true; + } searchResults = results; repaint(); } - }