From: Jim Procter Date: Fri, 23 Jan 2015 15:17:26 +0000 (+0000) Subject: JAL-1551 crlf changes X-Git-Tag: Jalview_2_9~108^2~3 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=5eb77715baf0d548c72385e13a3483cd63c36218 JAL-1551 crlf changes --- diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java index 8dd6290..3d1f7e2 100755 --- a/src/jalview/appletgui/SeqCanvas.java +++ b/src/jalview/appletgui/SeqCanvas.java @@ -1,830 +1,830 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 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 . - * The Jalview Authors are detailed in the 'AUTHORS' file. - */ -package jalview.appletgui; - -import jalview.datamodel.AlignmentI; -import jalview.datamodel.SearchResults; -import jalview.datamodel.SequenceGroup; -import jalview.datamodel.SequenceI; - -import java.awt.Color; -import java.awt.FontMetrics; -import java.awt.Graphics; -import java.awt.Image; -import java.awt.Panel; - -public class SeqCanvas extends Panel -{ - FeatureRenderer fr; - - SequenceRenderer sr; - - Image img; - - Graphics gg; - - int imgWidth; - - int imgHeight; - - AlignViewport av; - - SearchResults searchResults = null; - - boolean fastPaint = false; - - int cursorX = 0; - - int cursorY = 0; - - public SeqCanvas(AlignViewport av) - { - this.av = av; - fr = new FeatureRenderer(av); - sr = new SequenceRenderer(av); - PaintRefresher.Register(this, av.getSequenceSetId()); - } - - public AlignViewport getViewport() - { - return av; - } - - public FeatureRenderer getFeatureRenderer() - { - return fr; - } - - public SequenceRenderer getSequenceRenderer() - { - return sr; - } - - 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) - { - int value = i; - if (av.hasHiddenColumns()) - { - value = av.getColumnSelection().adjustForHiddenColumns(value); - } - - 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); - } - } - - void drawWestScale(Graphics g, int startx, int endx, int ypos) - { - FontMetrics fm = getFontMetrics(av.getFont()); - ypos += av.charHeight; - if (av.hasHiddenColumns()) - { - startx = av.getColumnSelection().adjustForHiddenColumns(startx); - endx = av.getColumnSelection().adjustForHiddenColumns(endx); - } - - int maxwidth = av.getAlignment().getWidth(); - if (av.hasHiddenColumns()) - { - maxwidth = av.getColumnSelection().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)) - - av.charWidth / 2; - g.drawString(value + "", x, (ypos + (i * av.charHeight)) - - (av.charHeight / 5)); - } - } - } - - void drawEastScale(Graphics g, int startx, int endx, int ypos) - { - ypos += av.charHeight; - - if (av.hasHiddenColumns()) - { - endx = av.getColumnSelection().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 * av.charHeight)) - - (av.charHeight / 5)); - } - } - } - - int lastsr = 0; - - void fastPaint(int horizontal, int vertical) - { - if (fastPaint || gg == null) - { - return; - } - - // Its possible on certain browsers that the call to fastpaint - // is faster than it can paint, so this check here catches - // this possibility - if (lastsr + horizontal != av.startRes) - { - horizontal = av.startRes - lastsr; - } - - lastsr = av.startRes; - - fastPaint = true; - gg.copyArea(horizontal * av.charWidth, vertical * av.charHeight, - imgWidth - horizontal * av.charWidth, imgHeight - vertical - * av.charHeight, -horizontal * av.charWidth, -vertical - * av.charHeight); - - int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0; - - if (horizontal > 0) // scrollbar pulled right, image to the left - { - transX = (er - sr - horizontal) * av.charWidth; - sr = er - horizontal; - } - else if (horizontal < 0) - { - er = sr - horizontal; - } - - else if (vertical > 0) // scroll down - { - ss = es - vertical; - if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time - { - ss = av.startSeq; - } - else - { - transY = imgHeight - vertical * av.charHeight; - } - } - else if (vertical < 0) - { - es = ss - vertical; - if (es > av.endSeq) - { - es = av.endSeq; - } - } - - gg.translate(transX, transY); - - drawPanel(gg, sr, er, ss, es, 0); - gg.translate(-transX, -transY); - - 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 update(Graphics g) - { - paint(g); - } - - public void paint(Graphics g) - { - - if (img != null - && (fastPaint || (getSize().width != g.getClipBounds().width) || (getSize().height != g - .getClipBounds().height))) - { - g.drawImage(img, 0, 0, this); - fastPaint = false; - return; - } - - if (fastPaint) - { - g.drawImage(img, 0, 0, this); - fastPaint = false; - return; - } - - // this draws the whole of the alignment - imgWidth = this.getSize().width; - imgHeight = this.getSize().height; - - imgWidth -= imgWidth % av.charWidth; - imgHeight -= imgHeight % av.charHeight; - - 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()); - } - - gg.setColor(Color.white); - gg.fillRect(0, 0, imgWidth, imgHeight); - - if (av.getWrapAlignment()) - { - drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes); - } - else - { - drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0); - } - - g.drawImage(img, 0, 0, this); - - } - - int LABEL_WEST, LABEL_EAST; - - public int getWrappedCanvasWidth(int cwidth) - { - cwidth -= cwidth % av.charWidth; - - FontMetrics fm = getFontMetrics(av.getFont()); - - LABEL_EAST = 0; - LABEL_WEST = 0; - - if (av.scaleRightWrapped) - { - LABEL_EAST = fm.stringWidth(getMask()); - } - - if (av.scaleLeftWrapped) - { - LABEL_WEST = fm.stringWidth(getMask()); - } - - return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth; - } - - /** - * Generates a string of zeroes. - * - * @return String - */ - String getMask() - { - String mask = "0"; - int maxWidth = 0; - int tmp; - AlignmentI alignment = av.getAlignment(); - for (int i = 0; i < alignment.getHeight(); i++) - { - tmp = alignment.getSequenceAt(i).getEnd(); - if (tmp > maxWidth) - { - maxWidth = tmp; - } - } - - for (int i = maxWidth; i > 0; i /= 10) - { - mask += "0"; - } - return mask; - } - - public void drawWrappedPanel(Graphics g, int canvasWidth, - int canvasHeight, int startRes) - { - AlignmentI al = av.getAlignment(); - - FontMetrics fm = getFontMetrics(av.getFont()); - - if (av.scaleRightWrapped) - { - LABEL_EAST = fm.stringWidth(getMask()); - } - - if (av.scaleLeftWrapped) - { - LABEL_WEST = fm.stringWidth(getMask()); - } - - int hgap = av.charHeight; - if (av.scaleAboveWrapped) - { - hgap += av.charHeight; - } - - int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth; - int cHeight = av.getAlignment().getHeight() * av.charHeight; - - av.setWrappedWidth(cWidth); - - av.endRes = av.startRes + cWidth; - - int endx; - int ypos = hgap; - - int maxwidth = av.getAlignment().getWidth() - 1; - - if (av.hasHiddenColumns()) - { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; - } - - while ((ypos <= canvasHeight) && (startRes < maxwidth)) - { - endx = startRes + cWidth - 1; - - if (endx > maxwidth) - { - endx = maxwidth; - } - - g.setColor(Color.black); - - 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); - - } - } - - if (g.getClip() == null) - { - g.setClip(0, 0, cWidth * av.charWidth, canvasHeight); - } - - drawPanel(g, startRes, endx, 0, al.getHeight(), ypos); - g.setClip(null); - - if (av.showAnnotation) - { - g.translate(0, cHeight + ypos + 4); - if (annotations == null) - { - annotations = new AnnotationPanel(av); - } - - annotations.drawComponent(g, startRes, endx + 1); - g.translate(0, -cHeight - ypos - 4); - } - 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); - } - - return annotations.adjustPanelHeight(); - } - - 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 - { - - int screenY = 0; - int blockStart = startRes; - int blockEnd = endRes; - - if (av.hasHiddenColumns()) - { - for (int[] region : av.getColumnSelection().getHiddenColumns()) - { - 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 = startSeq; i < endSeq; i++) - { - nextSeq = av.getAlignment().getSequenceAt(i); - - if (nextSeq == null) - { - continue; - } - - sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq), - startRes, endRes, offset + ((i - startSeq) * av.charHeight)); - - if (av.isShowSequenceFeatures()) - { - 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)); - } - } - } - - if (av.cursorMode && cursorY == i && cursorX >= startRes - && cursorX <= endRes) - { - sr.drawCursor(nextSeq, cursorX, - (cursorX - startRes) * av.charWidth, offset - + ((i - startSeq) * av.charHeight)); - } - } - - if (av.getSelectionGroup() != null - || av.getAlignment().getGroups().size() > 0) - { - drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset); - } - - } - - void drawGroupsBoundaries(Graphics g, int startRes, int endRes, - int startSeq, int endSeq, int offset) - { - // - // /////////////////////////////////// - // Now outline any areas if necessary - // /////////////////////////////////// - SequenceGroup group = av.getSelectionGroup(); - - int sx = -1; - int sy = -1; - int ex = -1; - int groupIndex = -1; - - if ((group == null) && (av.getAlignment().getGroups().size() > 0)) - { - group = av.getAlignment().getGroups().get(0); - groupIndex = 0; - } - - if (group != null) - { - do - { - int oldY = -1; - int i = 0; - boolean inGroup = false; - int top = -1; - int bottom = -1; - int alHeight = av.getAlignment().getHeight() - 1; - - for (i = startSeq; i < endSeq; i++) - { - sx = (group.getStartRes() - startRes) * av.charWidth; - sy = offset + ((i - startSeq) * av.charHeight); - ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) - 1; - - if (sx + ex < 0 || sx > imgWidth) - { - continue; - } - - if ((sx <= (endRes - startRes) * av.charWidth) - && group.getSequences(null).contains( - av.getAlignment().getSequenceAt(i))) - { - if ((bottom == -1) - && (i >= alHeight || !group.getSequences(null) - .contains( - av.getAlignment().getSequenceAt(i + 1)))) - { - bottom = sy + av.charHeight; - } - - if (!inGroup) - { - if (((top == -1) && (i == 0)) - || !group.getSequences(null).contains( - av.getAlignment().getSequenceAt(i - 1))) - { - top = sy; - } - - oldY = sy; - inGroup = true; - - if (group == av.getSelectionGroup()) - { - g.setColor(Color.red); - } - else - { - g.setColor(group.getOutlineColour()); - } - } - } - else - { - if (inGroup) - { - if (sx >= 0 && sx < imgWidth) - { - g.drawLine(sx, oldY, sx, sy); - } - - if (sx + ex < imgWidth) - { - g.drawLine(sx + ex, oldY, sx + ex, sy); - } - - if (sx < 0) - { - ex += sx; - sx = 0; - } - - if (sx + ex > imgWidth) - { - ex = imgWidth; - } - - 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; - } - - if (bottom != -1) - { - g.drawLine(sx, bottom, sx + ex, bottom); - bottom = -1; - } - - inGroup = false; - } - } - } - - if (inGroup) - { - sy = offset + ((i - startSeq) * av.charHeight); - if (sx >= 0 && sx < imgWidth) - { - g.drawLine(sx, oldY, sx, sy); - } - - if (sx + ex < imgWidth) - { - g.drawLine(sx + ex, oldY, sx + ex, sy); - } - - if (sx < 0) - { - ex += sx; - sx = 0; - } - - if (sx + ex > imgWidth) - { - ex = imgWidth; - } - 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; - } - - if (bottom != -1) - { - g.drawLine(sx, bottom - 1, sx + ex, bottom - 1); - bottom = -1; - } - - inGroup = false; - } - - groupIndex++; - - if (groupIndex >= av.getAlignment().getGroups().size()) - { - break; - } - - group = av.getAlignment().getGroups() - .get(groupIndex); - } while (groupIndex < av.getAlignment().getGroups().size()); - - } - } - - public void highlightSearchResults(SearchResults results) - { - searchResults = results; - - repaint(); - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.appletgui; + +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SearchResults; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; + +import java.awt.Color; +import java.awt.FontMetrics; +import java.awt.Graphics; +import java.awt.Image; +import java.awt.Panel; + +public class SeqCanvas extends Panel +{ + FeatureRenderer fr; + + SequenceRenderer sr; + + Image img; + + Graphics gg; + + int imgWidth; + + int imgHeight; + + AlignViewport av; + + SearchResults searchResults = null; + + boolean fastPaint = false; + + int cursorX = 0; + + int cursorY = 0; + + public SeqCanvas(AlignViewport av) + { + this.av = av; + fr = new FeatureRenderer(av); + sr = new SequenceRenderer(av); + PaintRefresher.Register(this, av.getSequenceSetId()); + } + + public AlignViewport getViewport() + { + return av; + } + + public FeatureRenderer getFeatureRenderer() + { + return fr; + } + + public SequenceRenderer getSequenceRenderer() + { + return sr; + } + + 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) + { + int value = i; + if (av.hasHiddenColumns()) + { + value = av.getColumnSelection().adjustForHiddenColumns(value); + } + + 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); + } + } + + void drawWestScale(Graphics g, int startx, int endx, int ypos) + { + FontMetrics fm = getFontMetrics(av.getFont()); + ypos += av.charHeight; + if (av.hasHiddenColumns()) + { + startx = av.getColumnSelection().adjustForHiddenColumns(startx); + endx = av.getColumnSelection().adjustForHiddenColumns(endx); + } + + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) + { + maxwidth = av.getColumnSelection().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)) + - av.charWidth / 2; + g.drawString(value + "", x, (ypos + (i * av.charHeight)) + - (av.charHeight / 5)); + } + } + } + + void drawEastScale(Graphics g, int startx, int endx, int ypos) + { + ypos += av.charHeight; + + if (av.hasHiddenColumns()) + { + endx = av.getColumnSelection().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 * av.charHeight)) + - (av.charHeight / 5)); + } + } + } + + int lastsr = 0; + + void fastPaint(int horizontal, int vertical) + { + if (fastPaint || gg == null) + { + return; + } + + // Its possible on certain browsers that the call to fastpaint + // is faster than it can paint, so this check here catches + // this possibility + if (lastsr + horizontal != av.startRes) + { + horizontal = av.startRes - lastsr; + } + + lastsr = av.startRes; + + fastPaint = true; + gg.copyArea(horizontal * av.charWidth, vertical * av.charHeight, + imgWidth - horizontal * av.charWidth, imgHeight - vertical + * av.charHeight, -horizontal * av.charWidth, -vertical + * av.charHeight); + + int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0; + + if (horizontal > 0) // scrollbar pulled right, image to the left + { + transX = (er - sr - horizontal) * av.charWidth; + sr = er - horizontal; + } + else if (horizontal < 0) + { + er = sr - horizontal; + } + + else if (vertical > 0) // scroll down + { + ss = es - vertical; + if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time + { + ss = av.startSeq; + } + else + { + transY = imgHeight - vertical * av.charHeight; + } + } + else if (vertical < 0) + { + es = ss - vertical; + if (es > av.endSeq) + { + es = av.endSeq; + } + } + + gg.translate(transX, transY); + + drawPanel(gg, sr, er, ss, es, 0); + gg.translate(-transX, -transY); + + 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 update(Graphics g) + { + paint(g); + } + + public void paint(Graphics g) + { + + if (img != null + && (fastPaint || (getSize().width != g.getClipBounds().width) || (getSize().height != g + .getClipBounds().height))) + { + g.drawImage(img, 0, 0, this); + fastPaint = false; + return; + } + + if (fastPaint) + { + g.drawImage(img, 0, 0, this); + fastPaint = false; + return; + } + + // this draws the whole of the alignment + imgWidth = this.getSize().width; + imgHeight = this.getSize().height; + + imgWidth -= imgWidth % av.charWidth; + imgHeight -= imgHeight % av.charHeight; + + 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()); + } + + gg.setColor(Color.white); + gg.fillRect(0, 0, imgWidth, imgHeight); + + if (av.getWrapAlignment()) + { + drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes); + } + else + { + drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0); + } + + g.drawImage(img, 0, 0, this); + + } + + int LABEL_WEST, LABEL_EAST; + + public int getWrappedCanvasWidth(int cwidth) + { + cwidth -= cwidth % av.charWidth; + + FontMetrics fm = getFontMetrics(av.getFont()); + + LABEL_EAST = 0; + LABEL_WEST = 0; + + if (av.scaleRightWrapped) + { + LABEL_EAST = fm.stringWidth(getMask()); + } + + if (av.scaleLeftWrapped) + { + LABEL_WEST = fm.stringWidth(getMask()); + } + + return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth; + } + + /** + * Generates a string of zeroes. + * + * @return String + */ + String getMask() + { + String mask = "0"; + int maxWidth = 0; + int tmp; + AlignmentI alignment = av.getAlignment(); + for (int i = 0; i < alignment.getHeight(); i++) + { + tmp = alignment.getSequenceAt(i).getEnd(); + if (tmp > maxWidth) + { + maxWidth = tmp; + } + } + + for (int i = maxWidth; i > 0; i /= 10) + { + mask += "0"; + } + return mask; + } + + public void drawWrappedPanel(Graphics g, int canvasWidth, + int canvasHeight, int startRes) + { + AlignmentI al = av.getAlignment(); + + FontMetrics fm = getFontMetrics(av.getFont()); + + if (av.scaleRightWrapped) + { + LABEL_EAST = fm.stringWidth(getMask()); + } + + if (av.scaleLeftWrapped) + { + LABEL_WEST = fm.stringWidth(getMask()); + } + + int hgap = av.charHeight; + if (av.scaleAboveWrapped) + { + hgap += av.charHeight; + } + + int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth; + int cHeight = av.getAlignment().getHeight() * av.charHeight; + + av.setWrappedWidth(cWidth); + + av.endRes = av.startRes + cWidth; + + int endx; + int ypos = hgap; + + int maxwidth = av.getAlignment().getWidth() - 1; + + if (av.hasHiddenColumns()) + { + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + } + + while ((ypos <= canvasHeight) && (startRes < maxwidth)) + { + endx = startRes + cWidth - 1; + + if (endx > maxwidth) + { + endx = maxwidth; + } + + g.setColor(Color.black); + + 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); + + } + } + + if (g.getClip() == null) + { + g.setClip(0, 0, cWidth * av.charWidth, canvasHeight); + } + + drawPanel(g, startRes, endx, 0, al.getHeight(), ypos); + g.setClip(null); + + if (av.showAnnotation) + { + g.translate(0, cHeight + ypos + 4); + if (annotations == null) + { + annotations = new AnnotationPanel(av); + } + + annotations.drawComponent(g, startRes, endx + 1); + g.translate(0, -cHeight - ypos - 4); + } + 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); + } + + return annotations.adjustPanelHeight(); + } + + 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 + { + + int screenY = 0; + int blockStart = startRes; + int blockEnd = endRes; + + if (av.hasHiddenColumns()) + { + for (int[] region : av.getColumnSelection().getHiddenColumns()) + { + 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 = startSeq; i < endSeq; i++) + { + nextSeq = av.getAlignment().getSequenceAt(i); + + if (nextSeq == null) + { + continue; + } + + sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq), + startRes, endRes, offset + ((i - startSeq) * av.charHeight)); + + if (av.isShowSequenceFeatures()) + { + 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)); + } + } + } + + if (av.cursorMode && cursorY == i && cursorX >= startRes + && cursorX <= endRes) + { + sr.drawCursor(nextSeq, cursorX, + (cursorX - startRes) * av.charWidth, offset + + ((i - startSeq) * av.charHeight)); + } + } + + if (av.getSelectionGroup() != null + || av.getAlignment().getGroups().size() > 0) + { + drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset); + } + + } + + void drawGroupsBoundaries(Graphics g, int startRes, int endRes, + int startSeq, int endSeq, int offset) + { + // + // /////////////////////////////////// + // Now outline any areas if necessary + // /////////////////////////////////// + SequenceGroup group = av.getSelectionGroup(); + + int sx = -1; + int sy = -1; + int ex = -1; + int groupIndex = -1; + + if ((group == null) && (av.getAlignment().getGroups().size() > 0)) + { + group = av.getAlignment().getGroups().get(0); + groupIndex = 0; + } + + if (group != null) + { + do + { + int oldY = -1; + int i = 0; + boolean inGroup = false; + int top = -1; + int bottom = -1; + int alHeight = av.getAlignment().getHeight() - 1; + + for (i = startSeq; i < endSeq; i++) + { + sx = (group.getStartRes() - startRes) * av.charWidth; + sy = offset + ((i - startSeq) * av.charHeight); + ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) - 1; + + if (sx + ex < 0 || sx > imgWidth) + { + continue; + } + + if ((sx <= (endRes - startRes) * av.charWidth) + && group.getSequences(null).contains( + av.getAlignment().getSequenceAt(i))) + { + if ((bottom == -1) + && (i >= alHeight || !group.getSequences(null) + .contains( + av.getAlignment().getSequenceAt(i + 1)))) + { + bottom = sy + av.charHeight; + } + + if (!inGroup) + { + if (((top == -1) && (i == 0)) + || !group.getSequences(null).contains( + av.getAlignment().getSequenceAt(i - 1))) + { + top = sy; + } + + oldY = sy; + inGroup = true; + + if (group == av.getSelectionGroup()) + { + g.setColor(Color.red); + } + else + { + g.setColor(group.getOutlineColour()); + } + } + } + else + { + if (inGroup) + { + if (sx >= 0 && sx < imgWidth) + { + g.drawLine(sx, oldY, sx, sy); + } + + if (sx + ex < imgWidth) + { + g.drawLine(sx + ex, oldY, sx + ex, sy); + } + + if (sx < 0) + { + ex += sx; + sx = 0; + } + + if (sx + ex > imgWidth) + { + ex = imgWidth; + } + + 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; + } + + if (bottom != -1) + { + g.drawLine(sx, bottom, sx + ex, bottom); + bottom = -1; + } + + inGroup = false; + } + } + } + + if (inGroup) + { + sy = offset + ((i - startSeq) * av.charHeight); + if (sx >= 0 && sx < imgWidth) + { + g.drawLine(sx, oldY, sx, sy); + } + + if (sx + ex < imgWidth) + { + g.drawLine(sx + ex, oldY, sx + ex, sy); + } + + if (sx < 0) + { + ex += sx; + sx = 0; + } + + if (sx + ex > imgWidth) + { + ex = imgWidth; + } + 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; + } + + if (bottom != -1) + { + g.drawLine(sx, bottom - 1, sx + ex, bottom - 1); + bottom = -1; + } + + inGroup = false; + } + + groupIndex++; + + if (groupIndex >= av.getAlignment().getGroups().size()) + { + break; + } + + group = av.getAlignment().getGroups() + .get(groupIndex); + } while (groupIndex < av.getAlignment().getGroups().size()); + + } + } + + public void highlightSearchResults(SearchResults results) + { + searchResults = results; + + repaint(); + } + +}