--/*
-- * 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 <http://www.gnu.org/licenses/>.
-- * 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
- {
- java.util.List<int[]> regions = av.getColumnSelection()
- .getHiddenColumns();
--
- int screenY = 0;
- int blockStart = startRes;
- int blockEnd = endRes;
--
- for (int i = 0; i < regions.size(); i++)
- {
- int[] region = regions.get(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 = 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();
- }
-
- }
- if (!av.hasHiddenColumns())
- {
- draw(g1, startRes, endRes, startSeq, endSeq, offset);
- }
- else
- {
-
-
-
- int screenY = 0;
- int blockStart = startRes;
- int blockEnd = endRes;
-
- if (av.getColumnSelection() != null
- && av.getColumnSelection().getHiddenColumns() != null)
- {
- java.util.Vector regions = av.getColumnSelection()
- .getHiddenColumns();
-
- 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 = 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();
- }
-
-}
++/*\r
++ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)\r
++ * Copyright (C) 2014 The Jalview Authors\r
++ * \r
++ * This file is part of Jalview.\r
++ * \r
++ * Jalview is free software: you can redistribute it and/or\r
++ * modify it under the terms of the GNU General Public License \r
++ * as published by the Free Software Foundation, either version 3\r
++ * of the License, or (at your option) any later version.\r
++ * \r
++ * Jalview is distributed in the hope that it will be useful, but \r
++ * WITHOUT ANY WARRANTY; without even the implied warranty \r
++ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
++ * PURPOSE. See the GNU General Public License for more details.\r
++ * \r
++ * You should have received a copy of the GNU General Public License\r
++ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
++ * The Jalview Authors are detailed in the 'AUTHORS' file.\r
++ */\r
++package jalview.appletgui;\r
++\r
++import jalview.datamodel.AlignmentI;\r
++import jalview.datamodel.SearchResults;\r
++import jalview.datamodel.SequenceGroup;\r
++import jalview.datamodel.SequenceI;\r
++\r
++import java.awt.Color;\r
++import java.awt.FontMetrics;\r
++import java.awt.Graphics;\r
++import java.awt.Image;\r
++import java.awt.Panel;\r
++\r
++public class SeqCanvas extends Panel\r
++{\r
++ FeatureRenderer fr;\r
++\r
++ SequenceRenderer sr;\r
++\r
++ Image img;\r
++\r
++ Graphics gg;\r
++\r
++ int imgWidth;\r
++\r
++ int imgHeight;\r
++\r
++ AlignViewport av;\r
++\r
++ SearchResults searchResults = null;\r
++\r
++ boolean fastPaint = false;\r
++\r
++ int cursorX = 0;\r
++\r
++ int cursorY = 0;\r
++\r
++ public SeqCanvas(AlignViewport av)\r
++ {\r
++ this.av = av;\r
++ fr = new FeatureRenderer(av);\r
++ sr = new SequenceRenderer(av);\r
++ PaintRefresher.Register(this, av.getSequenceSetId());\r
++ }\r
++\r
++ public AlignViewport getViewport()\r
++ {\r
++ return av;\r
++ }\r
++\r
++ public FeatureRenderer getFeatureRenderer()\r
++ {\r
++ return fr;\r
++ }\r
++\r
++ public SequenceRenderer getSequenceRenderer()\r
++ {\r
++ return sr;\r
++ }\r
++\r
++ void drawNorthScale(Graphics g, int startx, int endx, int ypos)\r
++ {\r
++ int scalestartx = startx - startx % 10 + 10;\r
++\r
++ g.setColor(Color.black);\r
++\r
++ // NORTH SCALE\r
++ for (int i = scalestartx; i < endx; i += 10)\r
++ {\r
++ int value = i;\r
++ if (av.hasHiddenColumns())\r
++ {\r
++ value = av.getColumnSelection().adjustForHiddenColumns(value);\r
++ }\r
++\r
++ g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth,\r
++ ypos - (av.charHeight / 2));\r
++\r
++ g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),\r
++ (ypos + 2) - (av.charHeight / 2),\r
++ ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),\r
++ ypos - 2);\r
++ }\r
++ }\r
++\r
++ void drawWestScale(Graphics g, int startx, int endx, int ypos)\r
++ {\r
++ FontMetrics fm = getFontMetrics(av.getFont());\r
++ ypos += av.charHeight;\r
++ if (av.hasHiddenColumns())\r
++ {\r
++ startx = av.getColumnSelection().adjustForHiddenColumns(startx);\r
++ endx = av.getColumnSelection().adjustForHiddenColumns(endx);\r
++ }\r
++\r
++ int maxwidth = av.getAlignment().getWidth();\r
++ if (av.hasHiddenColumns())\r
++ {\r
++ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
++ }\r
++\r
++ // WEST SCALE\r
++ for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
++ {\r
++ SequenceI seq = av.getAlignment().getSequenceAt(i);\r
++ int index = startx;\r
++ int value = -1;\r
++\r
++ while (index < endx)\r
++ {\r
++ if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
++ {\r
++ index++;\r
++\r
++ continue;\r
++ }\r
++\r
++ value = av.getAlignment().getSequenceAt(i).findPosition(index);\r
++\r
++ break;\r
++ }\r
++\r
++ if (value != -1)\r
++ {\r
++ int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))\r
++ - av.charWidth / 2;\r
++ g.drawString(value + "", x, (ypos + (i * av.charHeight))\r
++ - (av.charHeight / 5));\r
++ }\r
++ }\r
++ }\r
++\r
++ void drawEastScale(Graphics g, int startx, int endx, int ypos)\r
++ {\r
++ ypos += av.charHeight;\r
++\r
++ if (av.hasHiddenColumns())\r
++ {\r
++ endx = av.getColumnSelection().adjustForHiddenColumns(endx);\r
++ }\r
++\r
++ SequenceI seq;\r
++ // EAST SCALE\r
++ for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
++ {\r
++ seq = av.getAlignment().getSequenceAt(i);\r
++ int index = endx;\r
++ int value = -1;\r
++\r
++ while (index > startx)\r
++ {\r
++ if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
++ {\r
++ index--;\r
++\r
++ continue;\r
++ }\r
++\r
++ value = seq.findPosition(index);\r
++\r
++ break;\r
++ }\r
++\r
++ if (value != -1)\r
++ {\r
++ g.drawString(String.valueOf(value), 0, (ypos + (i * av.charHeight))\r
++ - (av.charHeight / 5));\r
++ }\r
++ }\r
++ }\r
++\r
++ int lastsr = 0;\r
++\r
++ void fastPaint(int horizontal, int vertical)\r
++ {\r
++ if (fastPaint || gg == null)\r
++ {\r
++ return;\r
++ }\r
++\r
++ // Its possible on certain browsers that the call to fastpaint\r
++ // is faster than it can paint, so this check here catches\r
++ // this possibility\r
++ if (lastsr + horizontal != av.startRes)\r
++ {\r
++ horizontal = av.startRes - lastsr;\r
++ }\r
++\r
++ lastsr = av.startRes;\r
++\r
++ fastPaint = true;\r
++ gg.copyArea(horizontal * av.charWidth, vertical * av.charHeight,\r
++ imgWidth - horizontal * av.charWidth, imgHeight - vertical\r
++ * av.charHeight, -horizontal * av.charWidth, -vertical\r
++ * av.charHeight);\r
++\r
++ int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0;\r
++\r
++ if (horizontal > 0) // scrollbar pulled right, image to the left\r
++ {\r
++ transX = (er - sr - horizontal) * av.charWidth;\r
++ sr = er - horizontal;\r
++ }\r
++ else if (horizontal < 0)\r
++ {\r
++ er = sr - horizontal;\r
++ }\r
++\r
++ else if (vertical > 0) // scroll down\r
++ {\r
++ ss = es - vertical;\r
++ if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time\r
++ {\r
++ ss = av.startSeq;\r
++ }\r
++ else\r
++ {\r
++ transY = imgHeight - vertical * av.charHeight;\r
++ }\r
++ }\r
++ else if (vertical < 0)\r
++ {\r
++ es = ss - vertical;\r
++ if (es > av.endSeq)\r
++ {\r
++ es = av.endSeq;\r
++ }\r
++ }\r
++\r
++ gg.translate(transX, transY);\r
++\r
++ drawPanel(gg, sr, er, ss, es, 0);\r
++ gg.translate(-transX, -transY);\r
++\r
++ repaint();\r
++\r
++ }\r
++\r
++ /**\r
++ * Definitions of startx and endx (hopefully): SMJS This is what I'm working\r
++ * towards! startx is the first residue (starting at 0) to display. endx is\r
++ * the last residue to display (starting at 0). starty is the first sequence\r
++ * to display (starting at 0). endy is the last sequence to display (starting\r
++ * at 0). NOTE 1: The av limits are set in setFont in this class and in the\r
++ * adjustment listener in SeqPanel when the scrollbars move.\r
++ */\r
++ public void update(Graphics g)\r
++ {\r
++ paint(g);\r
++ }\r
++\r
++ public void paint(Graphics g)\r
++ {\r
++\r
++ if (img != null\r
++ && (fastPaint || (getSize().width != g.getClipBounds().width) || (getSize().height != g\r
++ .getClipBounds().height)))\r
++ {\r
++ g.drawImage(img, 0, 0, this);\r
++ fastPaint = false;\r
++ return;\r
++ }\r
++\r
++ if (fastPaint)\r
++ {\r
++ g.drawImage(img, 0, 0, this);\r
++ fastPaint = false;\r
++ return;\r
++ }\r
++\r
++ // this draws the whole of the alignment\r
++ imgWidth = this.getSize().width;\r
++ imgHeight = this.getSize().height;\r
++\r
++ imgWidth -= imgWidth % av.charWidth;\r
++ imgHeight -= imgHeight % av.charHeight;\r
++\r
++ if (imgWidth < 1 || imgHeight < 1)\r
++ {\r
++ return;\r
++ }\r
++\r
++ if (img == null || imgWidth != img.getWidth(this)\r
++ || imgHeight != img.getHeight(this))\r
++ {\r
++ img = createImage(imgWidth, imgHeight);\r
++ gg = img.getGraphics();\r
++ gg.setFont(av.getFont());\r
++ }\r
++\r
++ gg.setColor(Color.white);\r
++ gg.fillRect(0, 0, imgWidth, imgHeight);\r
++\r
++ if (av.getWrapAlignment())\r
++ {\r
++ drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);\r
++ }\r
++ else\r
++ {\r
++ drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);\r
++ }\r
++\r
++ g.drawImage(img, 0, 0, this);\r
++\r
++ }\r
++\r
++ int LABEL_WEST, LABEL_EAST;\r
++\r
++ public int getWrappedCanvasWidth(int cwidth)\r
++ {\r
++ cwidth -= cwidth % av.charWidth;\r
++\r
++ FontMetrics fm = getFontMetrics(av.getFont());\r
++\r
++ LABEL_EAST = 0;\r
++ LABEL_WEST = 0;\r
++\r
++ if (av.scaleRightWrapped)\r
++ {\r
++ LABEL_EAST = fm.stringWidth(getMask());\r
++ }\r
++\r
++ if (av.scaleLeftWrapped)\r
++ {\r
++ LABEL_WEST = fm.stringWidth(getMask());\r
++ }\r
++\r
++ return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
++ }\r
++\r
++ /**\r
++ * Generates a string of zeroes.\r
++ * \r
++ * @return String\r
++ */\r
++ String getMask()\r
++ {\r
++ String mask = "0";\r
++ int maxWidth = 0;\r
++ int tmp;\r
++ AlignmentI alignment = av.getAlignment();\r
++ for (int i = 0; i < alignment.getHeight(); i++)\r
++ {\r
++ tmp = alignment.getSequenceAt(i).getEnd();\r
++ if (tmp > maxWidth)\r
++ {\r
++ maxWidth = tmp;\r
++ }\r
++ }\r
++\r
++ for (int i = maxWidth; i > 0; i /= 10)\r
++ {\r
++ mask += "0";\r
++ }\r
++ return mask;\r
++ }\r
++\r
++ public void drawWrappedPanel(Graphics g, int canvasWidth,\r
++ int canvasHeight, int startRes)\r
++ {\r
++ AlignmentI al = av.getAlignment();\r
++\r
++ FontMetrics fm = getFontMetrics(av.getFont());\r
++\r
++ if (av.scaleRightWrapped)\r
++ {\r
++ LABEL_EAST = fm.stringWidth(getMask());\r
++ }\r
++\r
++ if (av.scaleLeftWrapped)\r
++ {\r
++ LABEL_WEST = fm.stringWidth(getMask());\r
++ }\r
++\r
++ int hgap = av.charHeight;\r
++ if (av.scaleAboveWrapped)\r
++ {\r
++ hgap += av.charHeight;\r
++ }\r
++\r
++ int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
++ int cHeight = av.getAlignment().getHeight() * av.charHeight;\r
++\r
++ av.setWrappedWidth(cWidth);\r
++\r
++ av.endRes = av.startRes + cWidth;\r
++\r
++ int endx;\r
++ int ypos = hgap;\r
++\r
++ int maxwidth = av.getAlignment().getWidth() - 1;\r
++\r
++ if (av.hasHiddenColumns())\r
++ {\r
++ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
++ }\r
++\r
++ while ((ypos <= canvasHeight) && (startRes < maxwidth))\r
++ {\r
++ endx = startRes + cWidth - 1;\r
++\r
++ if (endx > maxwidth)\r
++ {\r
++ endx = maxwidth;\r
++ }\r
++\r
++ g.setColor(Color.black);\r
++\r
++ if (av.scaleLeftWrapped)\r
++ {\r
++ drawWestScale(g, startRes, endx, ypos);\r
++ }\r
++\r
++ if (av.scaleRightWrapped)\r
++ {\r
++ g.translate(canvasWidth - LABEL_EAST, 0);\r
++ drawEastScale(g, startRes, endx, ypos);\r
++ g.translate(-(canvasWidth - LABEL_EAST), 0);\r
++ }\r
++\r
++ g.translate(LABEL_WEST, 0);\r
++\r
++ if (av.scaleAboveWrapped)\r
++ {\r
++ drawNorthScale(g, startRes, endx, ypos);\r
++ }\r
++ if (av.hasHiddenColumns() && av.showHiddenMarkers)\r
++ {\r
++ g.setColor(Color.blue);\r
++ int res;\r
++ for (int i = 0; i < av.getColumnSelection().getHiddenColumns()\r
++ .size(); i++)\r
++ {\r
++ res = av.getColumnSelection().findHiddenRegionPosition(i)\r
++ - startRes;\r
++\r
++ if (res < 0 || res > endx - startRes)\r
++ {\r
++ continue;\r
++ }\r
++\r
++ gg.fillPolygon(new int[]\r
++ { res * av.charWidth - av.charHeight / 4,\r
++ res * av.charWidth + av.charHeight / 4, res * av.charWidth },\r
++ new int[]\r
++ { ypos - (av.charHeight / 2), ypos - (av.charHeight / 2),\r
++ ypos - (av.charHeight / 2) + 8 }, 3);\r
++\r
++ }\r
++ }\r
++\r
++ if (g.getClip() == null)\r
++ {\r
++ g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);\r
++ }\r
++\r
++ drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);\r
++ g.setClip(null);\r
++\r
++ if (av.showAnnotation)\r
++ {\r
++ g.translate(0, cHeight + ypos + 4);\r
++ if (annotations == null)\r
++ {\r
++ annotations = new AnnotationPanel(av);\r
++ }\r
++\r
++ annotations.drawComponent(g, startRes, endx + 1);\r
++ g.translate(0, -cHeight - ypos - 4);\r
++ }\r
++ g.translate(-LABEL_WEST, 0);\r
++\r
++ ypos += cHeight + getAnnotationHeight() + hgap;\r
++\r
++ startRes += cWidth;\r
++ }\r
++\r
++ }\r
++\r
++ AnnotationPanel annotations;\r
++\r
++ int getAnnotationHeight()\r
++ {\r
++ if (!av.showAnnotation)\r
++ {\r
++ return 0;\r
++ }\r
++\r
++ if (annotations == null)\r
++ {\r
++ annotations = new AnnotationPanel(av);\r
++ }\r
++\r
++ return annotations.adjustPanelHeight();\r
++ }\r
++\r
++ void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,\r
++ int endSeq, int offset)\r
++ {\r
++\r
++\r
++ if (!av.hasHiddenColumns())\r
++ {\r
++ draw(g1, startRes, endRes, startSeq, endSeq, offset);\r
++ }\r
++ else\r
++ {\r
++\r
++ int screenY = 0;\r
++ int blockStart = startRes;\r
++ int blockEnd = endRes;\r
++\r
++ if (av.hasHiddenColumns())\r
++ {\r
++ for (int[] region : av.getColumnSelection().getHiddenColumns())\r
++ {\r
++ int hideStart = region[0];\r
++ int hideEnd = region[1];\r
++\r
++ if (hideStart <= blockStart)\r
++ {\r
++ blockStart += (hideEnd - hideStart) + 1;\r
++ continue;\r
++ }\r
++\r
++ blockEnd = hideStart - 1;\r
++\r
++ g1.translate(screenY * av.charWidth, 0);\r
++\r
++ draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);\r
++\r
++ if (av.getShowHiddenMarkers())\r
++ {\r
++ g1.setColor(Color.blue);\r
++ g1.drawLine((blockEnd - blockStart + 1) * av.charWidth - 1,\r
++ 0 + offset, (blockEnd - blockStart + 1) * av.charWidth\r
++ - 1, (endSeq - startSeq) * av.charHeight\r
++ + offset);\r
++ }\r
++\r
++ g1.translate(-screenY * av.charWidth, 0);\r
++ screenY += blockEnd - blockStart + 1;\r
++ blockStart = hideEnd + 1;\r
++ }\r
++ }\r
++ if (screenY <= (endRes - startRes))\r
++ {\r
++ blockEnd = blockStart + (endRes - startRes) - screenY;\r
++ g1.translate(screenY * av.charWidth, 0);\r
++ draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);\r
++\r
++ g1.translate(-screenY * av.charWidth, 0);\r
++ }\r
++ }\r
++\r
++ }\r
++\r
++ // int startRes, int endRes, int startSeq, int endSeq, int x, int y,\r
++ // int x1, int x2, int y1, int y2, int startx, int starty,\r
++ void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq,\r
++ int offset)\r
++ {\r
++ g.setFont(av.getFont());\r
++ sr.prepare(g, av.renderGaps);\r
++\r
++ SequenceI nextSeq;\r
++\r
++ // / First draw the sequences\r
++ // ///////////////////////////\r
++ for (int i = startSeq; i < endSeq; i++)\r
++ {\r
++ nextSeq = av.getAlignment().getSequenceAt(i);\r
++\r
++ if (nextSeq == null)\r
++ {\r
++ continue;\r
++ }\r
++\r
++ sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),\r
++ startRes, endRes, offset + ((i - startSeq) * av.charHeight));\r
++\r
++ if (av.isShowSequenceFeatures())\r
++ {\r
++ fr.drawSequence(g, nextSeq, startRes, endRes, offset\r
++ + ((i - startSeq) * av.charHeight));\r
++ }\r
++\r
++ // / Highlight search Results once all sequences have been drawn\r
++ // ////////////////////////////////////////////////////////\r
++ if (searchResults != null)\r
++ {\r
++ int[] visibleResults = searchResults.getResults(nextSeq, startRes,\r
++ endRes);\r
++ if (visibleResults != null)\r
++ {\r
++ for (int r = 0; r < visibleResults.length; r += 2)\r
++ {\r
++ sr.drawHighlightedText(nextSeq, visibleResults[r],\r
++ visibleResults[r + 1], (visibleResults[r] - startRes)\r
++ * av.charWidth, offset\r
++ + ((i - startSeq) * av.charHeight));\r
++ }\r
++ }\r
++ }\r
++\r
++ if (av.cursorMode && cursorY == i && cursorX >= startRes\r
++ && cursorX <= endRes)\r
++ {\r
++ sr.drawCursor(nextSeq, cursorX,\r
++ (cursorX - startRes) * av.charWidth, offset\r
++ + ((i - startSeq) * av.charHeight));\r
++ }\r
++ }\r
++\r
++ if (av.getSelectionGroup() != null\r
++ || av.getAlignment().getGroups().size() > 0)\r
++ {\r
++ drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);\r
++ }\r
++\r
++ }\r
++\r
++ void drawGroupsBoundaries(Graphics g, int startRes, int endRes,\r
++ int startSeq, int endSeq, int offset)\r
++ {\r
++ //\r
++ // ///////////////////////////////////\r
++ // Now outline any areas if necessary\r
++ // ///////////////////////////////////\r
++ SequenceGroup group = av.getSelectionGroup();\r
++\r
++ int sx = -1;\r
++ int sy = -1;\r
++ int ex = -1;\r
++ int groupIndex = -1;\r
++\r
++ if ((group == null) && (av.getAlignment().getGroups().size() > 0))\r
++ {\r
++ group = av.getAlignment().getGroups().get(0);\r
++ groupIndex = 0;\r
++ }\r
++\r
++ if (group != null)\r
++ {\r
++ do\r
++ {\r
++ int oldY = -1;\r
++ int i = 0;\r
++ boolean inGroup = false;\r
++ int top = -1;\r
++ int bottom = -1;\r
++ int alHeight = av.getAlignment().getHeight() - 1;\r
++\r
++ for (i = startSeq; i < endSeq; i++)\r
++ {\r
++ sx = (group.getStartRes() - startRes) * av.charWidth;\r
++ sy = offset + ((i - startSeq) * av.charHeight);\r
++ ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) - 1;\r
++\r
++ if (sx + ex < 0 || sx > imgWidth)\r
++ {\r
++ continue;\r
++ }\r
++\r
++ if ((sx <= (endRes - startRes) * av.charWidth)\r
++ && group.getSequences(null).contains(\r
++ av.getAlignment().getSequenceAt(i)))\r
++ {\r
++ if ((bottom == -1)\r
++ && (i >= alHeight || !group.getSequences(null)\r
++ .contains(\r
++ av.getAlignment().getSequenceAt(i + 1))))\r
++ {\r
++ bottom = sy + av.charHeight;\r
++ }\r
++\r
++ if (!inGroup)\r
++ {\r
++ if (((top == -1) && (i == 0))\r
++ || !group.getSequences(null).contains(\r
++ av.getAlignment().getSequenceAt(i - 1)))\r
++ {\r
++ top = sy;\r
++ }\r
++\r
++ oldY = sy;\r
++ inGroup = true;\r
++\r
++ if (group == av.getSelectionGroup())\r
++ {\r
++ g.setColor(Color.red);\r
++ }\r
++ else\r
++ {\r
++ g.setColor(group.getOutlineColour());\r
++ }\r
++ }\r
++ }\r
++ else\r
++ {\r
++ if (inGroup)\r
++ {\r
++ if (sx >= 0 && sx < imgWidth)\r
++ {\r
++ g.drawLine(sx, oldY, sx, sy);\r
++ }\r
++\r
++ if (sx + ex < imgWidth)\r
++ {\r
++ g.drawLine(sx + ex, oldY, sx + ex, sy);\r
++ }\r
++\r
++ if (sx < 0)\r
++ {\r
++ ex += sx;\r
++ sx = 0;\r
++ }\r
++\r
++ if (sx + ex > imgWidth)\r
++ {\r
++ ex = imgWidth;\r
++ }\r
++\r
++ else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)\r
++ {\r
++ ex = (endRes - startRes + 1) * av.charWidth;\r
++ }\r
++\r
++ if (top != -1)\r
++ {\r
++ g.drawLine(sx, top, sx + ex, top);\r
++ top = -1;\r
++ }\r
++\r
++ if (bottom != -1)\r
++ {\r
++ g.drawLine(sx, bottom, sx + ex, bottom);\r
++ bottom = -1;\r
++ }\r
++\r
++ inGroup = false;\r
++ }\r
++ }\r
++ }\r
++\r
++ if (inGroup)\r
++ {\r
++ sy = offset + ((i - startSeq) * av.charHeight);\r
++ if (sx >= 0 && sx < imgWidth)\r
++ {\r
++ g.drawLine(sx, oldY, sx, sy);\r
++ }\r
++\r
++ if (sx + ex < imgWidth)\r
++ {\r
++ g.drawLine(sx + ex, oldY, sx + ex, sy);\r
++ }\r
++\r
++ if (sx < 0)\r
++ {\r
++ ex += sx;\r
++ sx = 0;\r
++ }\r
++\r
++ if (sx + ex > imgWidth)\r
++ {\r
++ ex = imgWidth;\r
++ }\r
++ else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)\r
++ {\r
++ ex = (endRes - startRes + 1) * av.charWidth;\r
++ }\r
++\r
++ if (top != -1)\r
++ {\r
++ g.drawLine(sx, top, sx + ex, top);\r
++ top = -1;\r
++ }\r
++\r
++ if (bottom != -1)\r
++ {\r
++ g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);\r
++ bottom = -1;\r
++ }\r
++\r
++ inGroup = false;\r
++ }\r
++\r
++ groupIndex++;\r
++\r
++ if (groupIndex >= av.getAlignment().getGroups().size())\r
++ {\r
++ break;\r
++ }\r
++\r
++ group = av.getAlignment().getGroups()\r
++ .get(groupIndex);\r
++ } while (groupIndex < av.getAlignment().getGroups().size());\r
++\r
++ }\r
++ }\r
++\r
++ public void highlightSearchResults(SearchResults results)\r
++ {\r
++ searchResults = results;\r
++\r
++ repaint();\r
++ }\r
++\r
++}\r
git://source.jalview.org / jalview.git / commitdiff